Graphical Solution of the Monic Quadratic Equation with Complex Coefficients

ERIC Educational Resources Information Center

Laine, A. D.

2015-01-01

There are many geometrical approaches to the solution of the quadratic equation with real coefficients. In this article it is shown that the monic quadratic equation with complex coefficients can also be solved graphically, by the intersection of two hyperbolas; one hyperbola being derived from the real part of the quadratic equation and one from…

IFITM3 requires an amphipathic helix for antiviral activity.

PubMed

Chesarino, Nicholas M; Compton, Alex A; McMichael, Temet M; Kenney, Adam D; Zhang, Lizhi; Soewarna, Victoria; Davis, Matthew; Schwartz, Olivier; Yount, Jacob S

2017-10-01

Interferon-induced transmembrane protein 3 (IFITM3) is a cellular factor that blocks virus fusion with cell membranes. IFITM3 has been suggested to alter membrane curvature and fluidity, though its exact mechanism of action is unclear. Using a bioinformatic approach, we predict IFITM3 secondary structures and identify a highly conserved, short amphipathic helix within a hydrophobic region of IFITM3 previously thought to be a transmembrane domain. Consistent with the known ability of amphipathic helices to alter membrane properties, we show that this helix and its amphipathicity are required for the IFITM3-dependent inhibition of influenza virus, Zika virus, vesicular stomatitis virus, Ebola virus, and human immunodeficiency virus infections. The homologous amphipathic helix within IFITM1 is also required for the inhibition of infection, indicating that IFITM proteins possess a conserved mechanism of antiviral action. We further demonstrate that the amphipathic helix of IFITM3 is required to block influenza virus hemagglutinin-mediated membrane fusion. Overall, our results provide evidence that IFITM proteins utilize an amphipathic helix for inhibiting virus fusion. © 2017 The Authors.

An Algorithm for Protein Helix Assignment Using Helix Geometry

PubMed Central

Cao, Chen; Xu, Shutan; Wang, Lincong

2015-01-01

Helices are one of the most common and were among the earliest recognized secondary structure elements in proteins. The assignment of helices in a protein underlies the analysis of its structure and function. Though the mathematical expression for a helical curve is simple, no previous assignment programs have used a genuine helical curve as a model for helix assignment. In this paper we present a two-step assignment algorithm. The first step searches for a series of bona fide helical curves each one best fits the coordinates of four successive backbone Cα atoms. The second step uses the best fit helical curves as input to make helix assignment. The application to the protein structures in the PDB (protein data bank) proves that the algorithm is able to assign accurately not only regular α-helix but also 310 and π helices as well as their left-handed versions. One salient feature of the algorithm is that the assigned helices are structurally more uniform than those by the previous programs. The structural uniformity should be useful for protein structure classification and prediction while the accurate assignment of a helix to a particular type underlies structure-function relationship in proteins. PMID:26132394

Unravelling Student Challenges with Quadratics: A Cognitive Approach

ERIC Educational Resources Information Center

Kotsopoulos, Donna

2007-01-01

The author's secondary school mathematics students have often reported to her that quadratic relations are one of the most conceptually challenging aspects of the high school curriculum. From her own classroom experiences there seemed to be several aspects to the students' challenges. Many students, even in their early secondary education, have…

Quadratic Optimisation with One Quadratic Equality Constraint

DTIC Science & Technology

2010-06-01

This report presents a theoretical framework for minimising a quadratic objective function subject to a quadratic equality constraint. The first part of the report gives a detailed algorithm which computes the global minimiser without calling special nonlinear optimisation solvers. The second part of the report shows how the developed theory can be applied to solve the time of arrival geolocation problem.

Linear state feedback, quadratic weights, and closed loop eigenstructures. M.S. Thesis

NASA Technical Reports Server (NTRS)

Thompson, P. M.

1979-01-01

Results are given on the relationships between closed loop eigenstructures, state feedback gain matrices of the linear state feedback problem, and quadratic weights of the linear quadratic regulator. Equations are derived for the angles of general multivariable root loci and linear quadratic optimal root loci, including angles of departure and approach. The generalized eigenvalue problem is used for the first time to compute angles of approach. Equations are also derived to find the sensitivity of closed loop eigenvalues and the directional derivatives of closed loop eigenvectors (with respect to a scalar multiplying the feedback gain matrix or the quadratic control weight). An equivalence class of quadratic weights that produce the same asymptotic eigenstructure is defined, sufficient conditions to be in it are given, a canonical element is defined, and an algorithm to find it is given. The behavior of the optimal root locus in the nonasymptotic region is shown to be different for quadratic weights with the same asymptotic properties.

A Unified Approach to Teaching Quadratic and Cubic Equations.

ERIC Educational Resources Information Center

Ward, A. J. B.

2003-01-01

Presents a simple method for teaching the algebraic solution of cubic equations via completion of the cube. Shows that this method is readily accepted by students already familiar with completion of the square as a method for quadratic equations. (Author/KHR)

Self-Replicating Quadratics

ERIC Educational Resources Information Center

Withers, Christopher S.; Nadarajah, Saralees

2012-01-01

We show that there are exactly four quadratic polynomials, Q(x) = x [superscript 2] + ax + b, such that (x[superscript 2] + ax + b) (x[superscript 2] - ax + b) = (x[superscript 4] + ax[superscript 2] + b). For n = 1, 2, ..., these quadratic polynomials can be written as the product of N = 2[superscript n] quadratic polynomials in x[superscript…

A new approach to approximating the linear quadratic optimal control law for hereditary systems with control delays

NASA Technical Reports Server (NTRS)

Milman, M. H.

1985-01-01

A factorization approach is presented for deriving approximations to the optimal feedback gain for the linear regulator-quadratic cost problem associated with time-varying functional differential equations with control delays. The approach is based on a discretization of the state penalty which leads to a simple structure for the feedback control law. General properties of the Volterra factors of Hilbert-Schmidt operators are then used to obtain convergence results for the feedback kernels.

Quadratic Damping

ERIC Educational Resources Information Center

Fay, Temple H.

2012-01-01

Quadratic friction involves a discontinuous damping term in equations of motion in order that the frictional force always opposes the direction of the motion. Perhaps for this reason this topic is usually omitted from beginning texts in differential equations and physics. However, quadratic damping is more realistic than viscous damping in many…

Using Linear and Quadratic Functions to Teach Number Patterns in Secondary School

ERIC Educational Resources Information Center

Kenan, Kok Xiao-Feng

2017-01-01

This paper outlines an approach to definitively find the general term in a number pattern, of either a linear or quadratic form, by using the general equation of a linear or quadratic function. This approach is governed by four principles: (1) identifying the position of the term (input) and the term itself (output); (2) recognising that each…

Converting One-Face α-Helix Mimetics into Amphiphilic α-Helix Mimetics as Potent Inhibitors of Protein-Protein Interactions.

PubMed

Lee, Ji Hoon; Oh, Misook; Kim, Hyun Soo; Lee, Huisun; Im, Wonpil; Lim, Hyun-Suk

2016-01-11

Many biologically active α-helical peptides adopt amphiphilic helical structures that contain hydrophobic residues on one side and hydrophilic residues on the other side. Therefore, α-helix mimetics capable of mimicking such amphiphilic helical peptides should possess higher binding affinity and specificity to target proteins. Here we describe an efficient method for generating amphiphilic α-helix mimetics. One-face α-helix mimetics having hydrophobic side chains on one side was readily converted into amphiphilic α-helix mimetics by introducing appropriate charged residues on the opposite side. We also demonstrate that such two-face amphiphilic α-helix mimetics indeed show remarkably improved binding affinity to a target protein, compared to one-face hydrophobic α-helix mimetics. We believe that generating a large combinatorial library of these amphiphilic α-helix mimetics can be valuable for rapid discovery of highly potent and specific modulators of protein-protein interactions.

Quadratic soliton self-reflection at a quadratically nonlinear interface

NASA Astrophysics Data System (ADS)

Jankovic, Ladislav; Kim, Hongki; Stegeman, George; Carrasco, Silvia; Torner, Lluis; Katz, Mordechai

2003-11-01

The reflection of bulk quadratic solutions incident onto a quadratically nonlinear interface in periodically poled potassium titanyl phosphate was observed. The interface consisted of the boundary between two quasi-phase-matched regions displaced from each other by a half-period. At high intensities and small angles of incidence the soliton is reflected.

Helix Nebula and CERN: A Symbiotic approach to exploiting commercial clouds

NASA Astrophysics Data System (ADS)

Barreiro Megino, Fernando H.; Jones, Robert; Kucharczyk, Katarzyna; Medrano Llamas, Ramón; van der Ster, Daniel

2014-06-01

The recent paradigm shift toward cloud computing in IT, and general interest in "Big Data" in particular, have demonstrated that the computing requirements of HEP are no longer globally unique. Indeed, the CERN IT department and LHC experiments have already made significant R&D investments in delivering and exploiting cloud computing resources. While a number of technical evaluations of interesting commercial offerings from global IT enterprises have been performed by various physics labs, further technical, security, sociological, and legal issues need to be address before their large-scale adoption by the research community can be envisaged. Helix Nebula - the Science Cloud is an initiative that explores these questions by joining the forces of three European research institutes (CERN, ESA and EMBL) with leading European commercial IT enterprises. The goals of Helix Nebula are to establish a cloud platform federating multiple commercial cloud providers, along with new business models, which can sustain the cloud marketplace for years to come. This contribution will summarize the participation of CERN in Helix Nebula. We will explain CERN's flagship use-case and the model used to integrate several cloud providers with an LHC experiment's workload management system. During the first proof of concept, this project contributed over 40.000 CPU-days of Monte Carlo production throughput to the ATLAS experiment with marginal manpower required. CERN's experience, together with that of ESA and EMBL, is providing a great insight into the cloud computing industry and highlighted several challenges that are being tackled in order to ease the export of the scientific workloads to the cloud environments.

Peptide mimics of the M13 coat protein transmembrane segment. Retention of helix-helix interaction motifs.

PubMed

Wang, C; Deber, C M

2000-05-26

Sequence-specific noncovalent helix-helix interactions between transmembrane (TM) segments in proteins are investigated by incorporating selected TM sequences into synthetic peptides using the construct CKKK-TM-KKK. The peptides are of suitable hydrophobicity for spontaneous membrane insertion, whereas formation of an N-terminal S-S bond can bring pairs of TM helices into proximity and promote their parallel orientation. Using the propensity of the protein to undergo thermally induced alpha-helix --> beta-sheet transitions as a parameter for helix stability, we compared the wild type and mutant (V29A and V31A) bacteriophage M13 coat proteins with their corresponding TM peptide constructs (M13 residues 24-42). Our results demonstrated that the relevant helix-helix tertiary contacts found in the intact proteins persist in the peptide mimics. Molecular dynamics simulations support the tight "two in-two out" dimerization motif for V31A consistent with mutagenesis data. The overall results reinforce the notion of TM segments as autonomous folding domains and suggest that the generic peptide construct provides a viable reductionist system for membrane protein structural and computational analysis.

Generating structured light with phase helix and intensity helix using reflection-enhanced plasmonic metasurface at 2 μm

NASA Astrophysics Data System (ADS)

Zhao, Yifan; Du, Jing; Zhang, Jinrun; Shen, Li; Wang, Jian

2018-04-01

Mid-infrared (2-20 μm) light has been attracting great attention in many areas of science and technology. Beyond the extended wavelength range from visible and near-infrared to mid-infrared, shaping spatial structures may add opportunities to grooming applications of mid-infrared photonics. Here, we design and fabricate a reflection-enhanced plasmonic metasurface and demonstrate efficient generation of structured light with the phase helix and intensity helix at 2 μm. This work includes two distinct aspects. First, structured light (phase helix, intensity helix) generation at 2 μm, which is far beyond the ability of conventional spatial light modulators, is enabled by the metasurface with sub-wavelength engineered structures. Second, the self-referenced intensity helix against environmental noise is generated without using a spatially separated light. The demonstrations may open up advanced perspectives to structured light applications at 2 μm, such as phase helix for communications and non-communications (imaging, sensing) and intensity helix for enhanced microscopy and advanced metrology.

Determining the Optimal Solution for Quadratically Constrained Quadratic Programming (QCQP) on Energy-Saving Generation Dispatch Problem

NASA Astrophysics Data System (ADS)

Lesmana, E.; Chaerani, D.; Khansa, H. N.

2018-03-01

Energy-Saving Generation Dispatch (ESGD) is a scheme made by Chinese Government in attempt to minimize CO2 emission produced by power plant. This scheme is made related to global warming which is primarily caused by too much CO2 in earth’s atmosphere, and while the need of electricity is something absolute, the power plants producing it are mostly thermal-power plant which produced many CO2. Many approach to fulfill this scheme has been made, one of them came through Minimum Cost Flow in which resulted in a Quadratically Constrained Quadratic Programming (QCQP) form. In this paper, ESGD problem with Minimum Cost Flow in QCQP form will be solved using Lagrange’s Multiplier Method

Structure of a protein G helix variant suggests the importance of helix propensity and helix dipole interactions in protein design.

PubMed Central

Strop, P.; Marinescu, A. M.; Mayo, S. L.

2000-01-01

Six helix surface positions of protein G (Gbeta1) were redesigned using a computational protein design algorithm, resulting in the five fold mutant Gbeta1m2. Gbeta1m2 is well folded with a circular dichroism spectrum nearly identical to that of Gbeta1, and a melting temperature of 91 degrees C, approximately 6 degrees C higher than that of Gbeta1. The crystal structure of Gbeta1m2 was solved to 2.0 A resolution by molecular replacement. The absence of hydrogen bond or salt bridge interactions between the designed residues in Gbeta1m2 suggests that the increased stability of Gbeta1m2 is due to increased helix propensity and more favorable helix dipole interactions. PMID:10933505

Quadratic correlation filters for optical correlators

NASA Astrophysics Data System (ADS)

Mahalanobis, Abhijit; Muise, Robert R.; Vijaya Kumar, Bhagavatula V. K.

2003-08-01

Linear correlation filters have been implemented in optical correlators and successfully used for a variety of applications. The output of an optical correlator is usually sensed using a square law device (such as a CCD array) which forces the output to be the squared magnitude of the desired correlation. It is however not a traditional practice to factor the effect of the square-law detector in the design of the linear correlation filters. In fact, the input-output relationship of an optical correlator is more accurately modeled as a quadratic operation than a linear operation. Quadratic correlation filters (QCFs) operate directly on the image data without the need for feature extraction or segmentation. In this sense, the QCFs retain the main advantages of conventional linear correlation filters while offering significant improvements in other respects. Not only is more processing required to detect peaks in the outputs of multiple linear filters, but choosing a winner among them is an error prone task. In contrast, all channels in a QCF work together to optimize the same performance metric and produce a combined output that leads to considerable simplification of the post-processing. In this paper, we propose a novel approach to the design of quadratic correlation based on the Fukunaga Koontz transform. Although quadratic filters are known to be optimum when the data is Gaussian, it is expected that they will perform as well as or better than linear filters in general. Preliminary performance results are provided that show that quadratic correlation filters perform better than their linear counterparts.

Helix-packing motifs in membrane proteins.

PubMed

Walters, R F S; DeGrado, W F

2006-09-12

The fold of a helical membrane protein is largely determined by interactions between membrane-imbedded helices. To elucidate recurring helix-helix interaction motifs, we dissected the crystallographic structures of membrane proteins into a library of interacting helical pairs. The pairs were clustered according to their three-dimensional similarity (rmsd helix-helix packing. Thus, the universe of common transmembrane helix-pairing motifs is relatively simple. The largest cluster, which comprises 29% of the library members, consists of an antiparallel motif with left-handed packing angles, and it is frequently stabilized by packing of small side chains occurring every seven residues in the sequence. Right-handed parallel and antiparallel structures show a similar tendency to segregate small residues to the helix-helix interface but spaced at four-residue intervals. Position-specific sequence propensities were derived for the most populated motifs. These structural and sequential motifs should be quite useful for the design and structural prediction of membrane proteins.

Conformational and dynamics simulation study of antimicrobial peptide hedistin-heterogeneity of its helix-turn-helix motif.

PubMed

Xu, Guohua; Wu, Min; Wang, Lin; Zhang, Xu; Cao, Shufen; Liu, Maili; Cui, Yanfang

2009-12-01

Hedistin is an antimicrobial peptide isolated from the coelomocytes of Nereis diversicolor, possessing activity against a large spectrum of bacteria including the methicillin resistant Staphylococcus aureus and Vibrio alginolyticus. The three-dimensional structure of hedistin in both aqueous solution and deuterated dodecylphosphocholine (DPC) micelles was examined using circular dichroism (CD) and nuclear magnetic resonance (NMR) techniques. And, the early events of the antibacterial process of hedistin were simulated using palmitoyl-oleoyl-phophatidylcholine (POPC) lipid bilayers and molecular dynamics (MD) simulation methods. Hedistin lacks secondary structure in aqueous solution, however, in DPC micelles, it features with a heterogeneous helix-turn-helix moiety and exhibits obvious amphipathic nature. The turn region (residues Val9-Thr12) in the moiety is a four-residue hinge, lying in between the first N-terminal alpha-helix (residues Leu5-Lys8) and the second alpha-helix (residues Val13-Ala17) regions and causing an approximately 120 degrees angle between the axes of the two helices. The segmental and nonlinear nature of hedistin structure is referred to as the heterogeneity of its helix-turn-helix motif which was found to be corresponding to a kind of discrete dynamics behavior, herein coined as its dynamical heterogeneity, at the early stage (0-50 ns) of the MD simulations. That is, the first helix segment, prior to (at 310 K) or following (at 363 K) the second helix, binds to the lipid head-group region and subsequently permeates into the hydrophobic lipid tail region, and the hinge is the last portion entering the lipid environment. This result implies that hedistin may adopt a "carpet" model action when disrupting bacterial membrane.

Chirality-specific lift forces of helix under shear flows: Helix perpendicular to shear plane.

PubMed

Zhang, Qi-Yi

2017-02-01

Chiral objects in shear flow experience a chirality-specific lift force. Shear flows past helices in a low Reynolds number regime were studied using slender-body theory. The chirality-specific lift forces in the vorticity direction experienced by helices are dominated by a set of helix geometry parameters: helix radius, pitch length, number of turns, and helix phase angle. Its analytical formula is given. The chirality-specific forces are the physical reasons for the chiral separation of helices in shear flow. Our results are well supported by the latest experimental observations. © 2016 Wiley Periodicals, Inc.

Electromagnetic tracking system with reduced distortion using quadratic excitation.

PubMed

Bien, Tomasz; Li, Mengfei; Salah, Zein; Rose, Georg

2014-03-01

Electromagnetic tracking systems, frequently used in minimally invasive surgery, are affected by conductive distorters. The influence of conductive distorters on electromagnetic tracking system accuracy can be reduced through magnetic field modifications. This approach was developed and tested. The voltage induced directly by the emitting coil in the sensing coil without additional influence by the conductive distorter depends on the first derivative of the voltage on the emitting coil. The voltage which is induced indirectly by the emitting coil across the conductive distorter in the sensing coil, however, depends on the second derivative of the voltage on the emitting coil. The electromagnetic tracking system takes advantage of this difference by supplying the emitting coil with a quadratic excitation voltage. The method is adaptive relative to the amount of distortion cause by the conductive distorters. This approach is evaluated with an experimental setup of the electromagnetic tracking system. In vitro testing showed that the maximal error decreased from 10.9 to 3.8 mm when the quadratic voltage was used to excite the emitting coil instead of the sinusoidal voltage. Furthermore, the root mean square error in the proximity of the aluminum disk used as a conductive distorter was reduced from 3.5 to 1.6 mm when the electromagnetic tracking system used the quadratic instead of sinusoidal excitation. Electromagnetic tracking with quadratic excitation is immune to the effects of a conductive distorter, especially compared with sinusoidal excitation of the emitting coil. Quadratic excitation of electromagnetic tracking for computer-assisted surgery is promising for clinical applications.

Hyperspectral and multispectral data fusion based on linear-quadratic nonnegative matrix factorization

NASA Astrophysics Data System (ADS)

Benhalouche, Fatima Zohra; Karoui, Moussa Sofiane; Deville, Yannick; Ouamri, Abdelaziz

2017-04-01

This paper proposes three multisharpening approaches to enhance the spatial resolution of urban hyperspectral remote sensing images. These approaches, related to linear-quadratic spectral unmixing techniques, use a linear-quadratic nonnegative matrix factorization (NMF) multiplicative algorithm. These methods begin by unmixing the observable high-spectral/low-spatial resolution hyperspectral and high-spatial/low-spectral resolution multispectral images. The obtained high-spectral/high-spatial resolution features are then recombined, according to the linear-quadratic mixing model, to obtain an unobservable multisharpened high-spectral/high-spatial resolution hyperspectral image. In the first designed approach, hyperspectral and multispectral variables are independently optimized, once they have been coherently initialized. These variables are alternately updated in the second designed approach. In the third approach, the considered hyperspectral and multispectral variables are jointly updated. Experiments, using synthetic and real data, are conducted to assess the efficiency, in spatial and spectral domains, of the designed approaches and of linear NMF-based approaches from the literature. Experimental results show that the designed methods globally yield very satisfactory spectral and spatial fidelities for the multisharpened hyperspectral data. They also prove that these methods significantly outperform the used literature approaches.

Quadrat Data for Fermilab Prairie Plant Survey

Science.gov Websites

Quadrat Data 2012 Quadrat Data 2013 Quadrat Data None taken by volunteers in 2014 due to weather problems . 2015 Quadrat Data 2016 Quadrat Data None taken by volunteers in 2017 due to weather and other problems

Triple helix purification and sequencing

DOEpatents

Wang, Renfeng; Smith, Lloyd M.; Tong, Xinchun E.

1995-01-01

Disclosed herein are methods, kits, and equipment for purifying single stranded circular DNA and then using the DNA for DNA sequencing purposes. Templates are provided with an insert having a hybridization region. An elongated oligonucleotide has two regions that are complementary to the insert and the oligo is bound to a magnetic anchor. The oligo hybridizes to the insert on two sides to form a stable triple helix complex. The anchor can then be used to drag the template out of solution using a magnet. The system can purify sequencing templates, and if desired the triple helix complex can be opened up to a double helix so that the oligonucleotide will act as a primer for further DNA synthesis.

Into the Eye of the Helix

NASA Astrophysics Data System (ADS)

2009-02-01

A deep new image of the magnificent Helix planetary nebula has been obtained using the Wide Field Imager at ESO's La Silla Observatory. The image shows a rich background of distant galaxies, usually not seen in other images of this object. ESO PR Photo 07a/09 The Helix Nebula ESO PR Video 06a/09 Helix Nebula Zoom-in ESO PR Video 06b/09 Pan over the Helix Nebula ESO PR Video 06c/09 Zoom and pan over the Helix Nebula The Helix Nebula, NGC 7293, lies about 700 light-years away in the constellation of Aquarius (the Water Bearer). It is one of the closest and most spectacular examples of a planetary nebula. These exotic objects have nothing to do with planets, but are the final blooming of Sun-like stars before their retirement as white dwarfs. Shells of gas are blown off from a star's surface, often in intricate and beautiful patterns, and shine under the harsh ultraviolet radiation from the faint, but very hot, central star. The main ring of the Helix Nebula is about two light-years across or half the distance between the Sun and its closest stellar neighbour. Despite being photographically very spectacular the Helix is hard to see visually as its light is thinly spread over a large area of sky and the history of its discovery is rather obscure. It first appears in a list of new objects compiled by the German astronomer Karl Ludwig Harding in 1824. The name Helix comes from the rough corkscrew shape seen in the earlier photographs. Although the Helix looks very much like a doughnut, studies have shown that it possibly consists of at least two separate discs with outer rings and filaments. The brighter inner disc seems to be expanding at about 100 000 km/h and to have taken about 12 000 years to have formed. Because the Helix is relatively close -- it covers an area of the sky about a quarter of the full Moon -- it can be studied in much greater detail than most other planetary nebulae and has been found to have an unexpected and complex structure. All around the

Democracy and environment as references for quadruple and quintuple helix innovation systems

NASA Astrophysics Data System (ADS)

Carayannis, Elias G.; Campbell, David F. J.; Orr, Barron J.

2015-04-01

The perspective of democracy and the ecological context define key references for knowledge production and innovation in innovation systems. Particularly under conditions of environmental change where enhancing the potential for adaptation is critical, this requires a closer look at ecological responsibility and sensitivity in the different innovation models and governance regimes. The "Quintuple Helix" innovation model is an approach that stresses the necessary socio-ecological transition of society and economy by adding an environment helix to an innovation system already made up of three (university-industry-government) or four (civil society relations) helices in a way that supports adaptation by incorporating global warming as both a challenge to and a driver of innovation. There is the proposition that knowledge production and innovation co-evolve with democracy (Carayannis and Campbell, 2014). In the Triple Helix model (Etzkowitz and Leydesdorff, 2000) the existence of a democracy does not appear to be necessary for knowledge production and innovation. However, the Quadruple Helix (Carayannis and Campbell, 2009, 2010 and 2014) is defined and represented by additional key attributes and components: "media-based and culture-based public", "civil society" and "arts, artistic research and arts-based innovation" (Bast, Carayannis and Campbell, 2015). Implications of this are that the fourth helix in the Quadruple Helix innovation systems brings in and represents the perspective of "dimension of democracy" or the "context of democracy" for knowledge in general and knowledge production and innovation in more particular. Within theories of democracy there is a competition between narrow and broader concepts of democracy (Campbell, 2013). This is particularly true when democracy is to be understood to transcend more substantially the narrow understanding of being primarily based on or being primarily rooted in government institutions (within a Triple Helix

Non-planar one-loop Parke-Taylor factors in the CHY approach for quadratic propagators

NASA Astrophysics Data System (ADS)

Ahmadiniaz, Naser; Gomez, Humberto; Lopez-Arcos, Cristhiam

2018-05-01

In this work we have studied the Kleiss-Kuijf relations for the recently introduced Parke-Taylor factors at one-loop in the CHY approach, that reproduce quadratic Feynman propagators. By doing this, we were able to identify the non-planar one-loop Parke-Taylor factors. In order to check that, in fact, these new factors can describe non-planar amplitudes, we applied them to the bi-adjoint Φ3 theory. As a byproduct, we found a new type of graphs that we called the non-planar CHY-graphs. These graphs encode all the information for the subleading order at one-loop, and there is not an equivalent of these in the Feynman formalism.

Probabilistic grammatical model for helix‐helix contact site classification

PubMed Central

2013-01-01

Background Hidden Markov Models power many state‐of‐the‐art tools in the field of protein bioinformatics. While excelling in their tasks, these methods of protein analysis do not convey directly information on medium‐ and long‐range residue‐residue interactions. This requires an expressive power of at least context‐free grammars. However, application of more powerful grammar formalisms to protein analysis has been surprisingly limited. Results In this work, we present a probabilistic grammatical framework for problem‐specific protein languages and apply it to classification of transmembrane helix‐helix pairs configurations. The core of the model consists of a probabilistic context‐free grammar, automatically inferred by a genetic algorithm from only a generic set of expert‐based rules and positive training samples. The model was applied to produce sequence based descriptors of four classes of transmembrane helix‐helix contact site configurations. The highest performance of the classifiers reached AUCROC of 0.70. The analysis of grammar parse trees revealed the ability of representing structural features of helix‐helix contact sites. Conclusions We demonstrated that our probabilistic context‐free framework for analysis of protein sequences outperforms the state of the art in the task of helix‐helix contact site classification. However, this is achieved without necessarily requiring modeling long range dependencies between interacting residues. A significant feature of our approach is that grammar rules and parse trees are human‐readable. Thus they could provide biologically meaningful information for molecular biologists. PMID:24350601

Triple helix purification and sequencing

DOEpatents

Wang, R.; Smith, L.M.; Tong, X.E.

1995-03-28

Disclosed herein are methods, kits, and equipment for purifying single stranded circular DNA and then using the DNA for DNA sequencing purposes. Templates are provided with an insert having a hybridization region. An elongated oligonucleotide has two regions that are complementary to the insert and the oligo is bound to a magnetic anchor. The oligo hybridizes to the insert on two sides to form a stable triple helix complex. The anchor can then be used to drag the template out of solution using a magnet. The system can purify sequencing templates, and if desired the triple helix complex can be opened up to a double helix so that the oligonucleotide will act as a primer for further DNA synthesis. 4 figures.

Effect of polarization on the stability of a helix dimer

NASA Astrophysics Data System (ADS)

Wang, Xing Y.; Zhang, John Z. H.

2011-01-01

Molecular dynamics (MD) simulations have been carried out to study helix-helix interaction using both standard AMBER and polarized force fields. Comparison of the two simulations shows that electrostatic polarization of intra-protein hydrogen bonds plays a significant role in stabilizing the structure of helix dimer. This stabilizing effect is clearly demonstrated by examining the monomer structure, helix crossing angle and stability of backbone hydrogen bonds under AMBER and PPC. Since reliable prediction of protein-protein structure is a significant challenge, the current study should help shed light on the importance of electrostatic polarization of protein in helix-helix interaction and helix bundle structures.

Learning quadratic receptive fields from neural responses to natural stimuli.

PubMed

Rajan, Kanaka; Marre, Olivier; Tkačik, Gašper

2013-07-01

Models of neural responses to stimuli with complex spatiotemporal correlation structure often assume that neurons are selective for only a small number of linear projections of a potentially high-dimensional input. In this review, we explore recent modeling approaches where the neural response depends on the quadratic form of the input rather than on its linear projection, that is, the neuron is sensitive to the local covariance structure of the signal preceding the spike. To infer this quadratic dependence in the presence of arbitrary (e.g., naturalistic) stimulus distribution, we review several inference methods, focusing in particular on two information theory-based approaches (maximization of stimulus energy and of noise entropy) and two likelihood-based approaches (Bayesian spike-triggered covariance and extensions of generalized linear models). We analyze the formal relationship between the likelihood-based and information-based approaches to demonstrate how they lead to consistent inference. We demonstrate the practical feasibility of these procedures by using model neurons responding to a flickering variance stimulus.

The swimming of a perfect deforming helix

NASA Astrophysics Data System (ADS)

Koens, Lyndon; Zhang, Hang; Mourran, Ahmed; Lauga, Eric

2017-11-01

Many bacteria rotate helical flagellar filaments in order to swim. When at rest or rotated counter-clockwise these flagella are left handed helices but they undergo polymorphic transformations to right-handed helices when the motor is reversed. These helical deformations themselves can generate motion, with for example Rhodobacter sphaeroides using the polymorphic transformation of the flagellum to generate rotation, or Spiroplasma propagating a change of helix handedness across its body's length to generate forward motion. Recent experiments reported on an artificial helical microswimmer generating motion without a propagating change in handedness. Made of a temperature sensitive gel, these swimmers moved by changing the dimensions of the helix in a non-reciprocal way. Inspired by these results and helix's ubiquitous presence in the bacterial world, we investigate how a deforming helix moves within a viscous fluid. Maintaining a single handedness along its entire length, we discuss how a perfect deforming helix can create a non-reciprocal swimming stroke, identify its principle directions of motion, and calculate the swimming kinematics asymptotically.

Quadratic spline subroutine package

USGS Publications Warehouse

Rasmussen, Lowell A.

1982-01-01

A continuous piecewise quadratic function with continuous first derivative is devised for approximating a single-valued, but unknown, function represented by a set of discrete points. The quadratic is proposed as a treatment intermediate between using the angular (but reliable, easily constructed and manipulated) piecewise linear function and using the smoother (but occasionally erratic) cubic spline. Neither iteration nor the solution of a system of simultaneous equations is necessary to determining the coefficients. Several properties of the quadratic function are given. A set of five short FORTRAN subroutines is provided for generating the coefficients (QSC), finding function value and derivatives (QSY), integrating (QSI), finding extrema (QSE), and computing arc length and the curvature-squared integral (QSK). (USGS)

Anderson transition in a multiply-twisted helix.

PubMed

Ugajin, R

2001-06-01

We investigated the Anderson transition in a multiply-twisted helix in which a helical chain of components, i.e., atoms or nanoclusters, is twisted to produce a doubly-twisted helix, which itself can be twisted to produce a triply-twisted helix, and so on, in which there are couplings between adjacent rounds of helices. As the strength of the on-site random potentials increases, an Anderson transition occurs, suggesting that the number of dimensions is 3 for electrons running along the multiply-twisted helix when the couplings between adjacent rounds are strong enough. If the couplings are weakened, the dimensionality becomes less, resulting in localization of electrons. The effect of random connections between adjacent rounds of helices and random magnetic fields that thread the structure is analyzed using the spectral statistics of a quantum particle.

Measurement of the quadratic hyperpolarizability of the collagen triple helix and application to second harmonic imaging of natural and biomimetic collagenous tissues

NASA Astrophysics Data System (ADS)

Deniset-Besseau, A.; Strupler, M.; Duboisset, J.; De Sa Peixoto, P.; Benichou, E.; Fligny, C.; Tharaux, P.-L.; Mosser, G.; Brevet, P.-F.; Schanne-Klein, M.-C.

2009-09-01

Collagen is a major protein of the extracellular matrix that is characterized by triple helical domains. It plays a central role in the formation of fibrillar and microfibrillar networks, basement membranes, as well as other structures of the connective tissue. Remarkably, fibrillar collagen exhibits efficient Second Harmonic Generation (SHG) so that SHG microscopy proved to be a sensitive tool to probe the three-dimensional architecture of fibrillar collagen and to assess the progression of fibrotic pathologies. We obtained sensitive and reproducible measurements of the fibrosis extent, but we needed quantitative data at the molecular level to further process SHG images. We therefore performed Hyper- Rayleigh Scattering (HRS) experiments and measured a second order hyperpolarisability of 1.25 10-27 esu for rat-tail type I collagen. This value is surprisingly large considering that collagen presents no strong harmonophore in its aminoacid sequence. In order to get insight into the physical origin of this nonlinear process, we performed HRS measurements after denaturation of the collagen triple helix and for a collagen-like short model peptide [(Pro-Pro- Gly)10]3. It showed that the collagen large nonlinear response originates in the tight alignment of a large number of weakly efficient harmonophores, presumably the peptide bonds, resulting in a coherent amplification of the nonlinear signal along the triple helix. To illustrate this mechanism, we successfully recorded SHG images in collagenous biomimetic matrices.

Probing sequence dependence of folding pathway of α-helix bundle proteins through free energy landscape analysis.

PubMed

Shao, Qiang

2014-06-05

A comparative study on the folding of multiple three-α-helix bundle proteins including α3D, α3W, and the B domain of protein A (BdpA) is presented. The use of integrated-tempering-sampling molecular dynamics simulations achieves reversible folding and unfolding events in individual short trajectories, which thus provides an efficient approach to sufficiently sample the configuration space of protein and delineate the folding pathway of α-helix bundle. The detailed free energy landscape analyses indicate that the folding mechanism of α-helix bundle is not uniform but sequence dependent. A simple model is then proposed to predict folding mechanism of α-helix bundle on the basis of amino acid composition: α-helical proteins containing higher percentage of hydrophobic residues than charged ones fold via nucleation-condensation mechanism (e.g., α3D and BdpA) whereas proteins having opposite tendency in amino acid composition more likely fold via the framework mechanism (e.g., α3W). The model is tested on various α-helix bundle proteins, and the predicted mechanism is similar to the most approved one for each protein. In addition, the common features in the folding pathway of α-helix bundle protein are also deduced. In summary, the present study provides comprehensive, atomic-level picture of the folding of α-helix bundle proteins.

Linear state feedback, quadratic weights, and closed loop eigenstructures. M.S. Thesis. Final Report

NASA Technical Reports Server (NTRS)

Thompson, P. M.

1980-01-01

Equations are derived for the angles of general multivariable root loci and linear quadratic optimal root loci, including angles of departure and approach. The generalized eigenvalue problem is used to compute angles of approach. Equations are also derived to find the sensitivity of closed loop eigenvalue and the directional derivatives of closed loop eigenvectors. An equivalence class of quadratic weights that produce the same asymptotic eigenstructure is defined, a canonical element is defined, and an algorithm to find it is given. The behavior of the optimal root locus in the nonasymptotic region is shown to be different for quadratic weights with the same asymptotic properties. An algorithm is presented that can be used to select a feedback gain matrix for the linear state feedback problem which produces a specified asymptotic eigenstructure. Another algorithm is given to compute the asymptotic eigenstructure properties inherent in a given set of quadratic weights. Finally, it is shown that optimal root loci for nongeneric problems can be approximated by generic ones in the nonasymptotic region.

Designing cooperatively folded abiotic uni- and multimolecular helix bundles

NASA Astrophysics Data System (ADS)

de, Soumen; Chi, Bo; Granier, Thierry; Qi, Ting; Maurizot, Victor; Huc, Ivan

2018-01-01

Abiotic foldamers, that is foldamers that have backbones chemically remote from peptidic and nucleotidic skeletons, may give access to shapes and functions different to those of peptides and nucleotides. However, design methodologies towards abiotic tertiary and quaternary structures are yet to be developed. Here we report rationally designed interactional patterns to guide the folding and assembly of abiotic helix bundles. Computational design facilitated the introduction of hydrogen-bonding functionalities at defined locations on the aromatic amide backbones that promote cooperative folding into helix-turn-helix motifs in organic solvents. The hydrogen-bond-directed aggregation of helices not linked by a turn unit produced several thermodynamically and kinetically stable homochiral dimeric and trimeric bundles with structures that are distinct from the designed helix-turn-helix. Relative helix orientation within the bundles may be changed from parallel to tilted on subtle solvent variations. Altogether, these results prefigure the richness and uniqueness of abiotic tertiary structure behaviour.

Complex between triple helix of collagen and double helix of DNA in aqueous solution.

PubMed

Mrevlishvili, George M; Svintradze, David V

2005-06-01

We demonstrate in this paper that one example of a biologically important and molecular self-assembling complex system is a collagen-DNA ordered aggregate which spontaneously forms in aqueous solutions. Interaction between the collagen and the DNA leads to destruction of the hydration shell of the triple helix and stabilization of the double helix structure. From a molecular biology point of view this nano-scale self-assembling superstructure could increase the stability of DNA against the nucleases during collagen diseases and the growth of collagen fibrills in the presence of DNA.

The helix bundle: A reversible lipid binding motif

PubMed Central

Narayanaswami, Vasanthy; Kiss, Robert S.; Weers, Paul M.M.

2009-01-01

Apolipoproteins are the protein components of lipoproteins that have the innate ability to inter convert between a lipid-free and a lipid-bound form in a facile manner, a remarkable property conferred by the helix bundle motif. Composed of a series of four or five amphipathic α-helices that fold to form a helix bundle, this motif allows the en face orientation of the hydrophobic faces of the α-helices in the protein interior in the lipid-free state. A conformational switch then permits helix-helix interactions to be substituted by helix-lipid interactions upon lipid binding interaction. This review compares the apolipoprotein high resolution structures and the factors that trigger this switch in insect apolipophorin III and the mammalian apolipoproteins, apolipoprotein E and apolipoprotein A-I, pointing out the commonalities and key differences in the mode of lipid interaction. Further insights into the lipid bound conformation of apolipoproteins are required to fully understand their functional role under physiological conditions. PMID:19770066

Finding the Best Quadratic Approximation of a Function

ERIC Educational Resources Information Center

Yang, Yajun; Gordon, Sheldon P.

2011-01-01

This article examines the question of finding the best quadratic function to approximate a given function on an interval. The prototypical function considered is f(x) = e[superscript x]. Two approaches are considered, one based on Taylor polynomial approximations at various points in the interval under consideration, the other based on the fact…

Interactions between relay helix and Src homology 1 domain helix (SH1) drive the converter domain rotation during the recovery stroke of myosin II

PubMed Central

Baumketner, Andrij

2012-01-01

Myosin motor protein exists in two alternative conformations, pre-recovery state M* and post-recovery state M**, upon ATP binding. The details of the M*-to-M** transition, known as the recovery stroke to reflect its role as the functional opposite of the force-generating power stroke, remain elusive. The defining feature of the post-recovery state is a kink in the relay helix, a key part of the protein involved in force generation. In this paper we determine the interactions that are responsible for the appearance of the kink. We design a series of computational models that contain three other segments, relay loop, converter domain and Src homology 1 domain helix (SH1), with which relay helix interacts, and determine their structure in accurate replica exchange molecular dynamics simulations in explicit solvent. By conducting an exhaustive combinatorial search among different models we find that: 1) the converter domain must be attached to the relay helix during the transition, so it does not interfere with other parts of the protein, 2) the structure of the relay helix is controlled by SH1 helix. The kink is strongly coupled to the position of SH1 helix. It arises as a result of direct interactions between SH1 and the relay helix and leads to a rotation of the C-terminal part of the relay helix which is subsequently transmitted to the converter domain. PMID:22411190

An auto-inhibitory helix in CTP:phosphocholine cytidylyltransferase hijacks the catalytic residue and constrains a pliable, domain-bridging helix pair

PubMed Central

Ramezanpour, Mohsen; Lee, Jaeyong; Taneva, Svetla G.; Tieleman, D. Peter; Cornell, Rosemary B.

2018-01-01

The activity of CTP:phosphocholine cytidylyltransferase (CCT), a key enzyme in phosphatidylcholine synthesis, is regulated by reversible interactions of a lipid-inducible amphipathic helix (domain M) with membrane phospholipids. When dissociated from membranes, a portion of the M domain functions as an auto-inhibitory (AI) element to suppress catalysis. The AI helix from each subunit binds to a pair of α helices (αE) that extend from the base of the catalytic dimer to create a four-helix bundle. The bound AI helices make intimate contact with loop L2, housing a key catalytic residue, Lys122. The impacts of the AI helix on active-site dynamics and positioning of Lys122 are unknown. Extensive MD simulations with and without the AI helix revealed that backbone carbonyl oxygens at the point of contact between the AI helix and loop L2 can entrap the Lys122 side chain, effectively competing with the substrate, CTP. In silico, removal of the AI helices dramatically increased αE dynamics at a predicted break in the middle of these helices, enabling them to splay apart and forge new contacts with loop L2. In vitro cross-linking confirmed the reorganization of the αE element upon membrane binding of the AI helix. Moreover, when αE bending was prevented by disulfide engineering, CCT activation by membrane binding was thwarted. These findings suggest a novel two-part auto-inhibitory mechanism for CCT involving capture of Lys122 and restraint of the pliable αE helices. We propose that membrane binding enables bending of the αE helices, bringing the active site closer to the membrane surface. PMID:29519816

Piece-wise quadratic approximations of arbitrary error functions for fast and robust machine learning.

PubMed

Gorban, A N; Mirkes, E M; Zinovyev, A

2016-12-01

Most of machine learning approaches have stemmed from the application of minimizing the mean squared distance principle, based on the computationally efficient quadratic optimization methods. However, when faced with high-dimensional and noisy data, the quadratic error functionals demonstrated many weaknesses including high sensitivity to contaminating factors and dimensionality curse. Therefore, a lot of recent applications in machine learning exploited properties of non-quadratic error functionals based on L 1 norm or even sub-linear potentials corresponding to quasinorms L p (0approaches is increase in computational cost for optimization. Till so far, no approaches have been suggested to deal with arbitrary error functionals, in a flexible and computationally efficient framework. In this paper, we develop a theory and basic universal data approximation algorithms (k-means, principal components, principal manifolds and graphs, regularized and sparse regression), based on piece-wise quadratic error potentials of subquadratic growth (PQSQ potentials). We develop a new and universal framework to minimize arbitrary sub-quadratic error potentials using an algorithm with guaranteed fast convergence to the local or global error minimum. The theory of PQSQ potentials is based on the notion of the cone of minorant functions, and represents a natural approximation formalism based on the application of min-plus algebra. The approach can be applied in most of existing machine learning methods, including methods of data approximation and regularized and sparse regression, leading to the improvement in the computational cost/accuracy trade-off. We demonstrate that on synthetic and real-life datasets PQSQ-based machine learning methods achieve orders of magnitude faster computational performance than the corresponding state-of-the-art methods, having similar or better approximation accuracy. Copyright © 2016 Elsevier Ltd. All rights reserved.

One-loop Parke-Taylor factors for quadratic propagators from massless scattering equations

NASA Astrophysics Data System (ADS)

Gomez, Humberto; Lopez-Arcos, Cristhiam; Talavera, Pedro

2017-10-01

In this paper we reconsider the Cachazo-He-Yuan construction (CHY) of the so called scattering amplitudes at one-loop, in order to obtain quadratic propagators. In theories with colour ordering the key ingredient is the redefinition of the Parke-Taylor factors. After classifying all the possible one-loop CHY-integrands we conjecture a new one-loop amplitude for the massless Bi-adjoint Φ3 theory. The prescription directly reproduces the quadratic propagators of the traditional Feynman approach.

The Factorability of Quadratics: Motivation for More Techniques

ERIC Educational Resources Information Center

Bosse, Michael J.; Nandakumar, N. R.

2005-01-01

Typically, secondary and college algebra students attempt to utilize either completing the square or the quadratic formula as techniques to solve a quadratic equation only after frustration with factoring has arisen. While both completing the square and the quadratic formula are techniques which can determine solutions for all quadratic equations,…

Predicting helix–helix interactions from residue contacts in membrane proteins

PubMed Central

Lo, Allan; Chiu, Yi-Yuan; Rødland, Einar Andreas; Lyu, Ping-Chiang; Sung, Ting-Yi; Hsu, Wen-Lian

2009-01-01

Motivation: Helix–helix interactions play a critical role in the structure assembly, stability and function of membrane proteins. On the molecular level, the interactions are mediated by one or more residue contacts. Although previous studies focused on helix-packing patterns and sequence motifs, few of them developed methods specifically for contact prediction. Results: We present a new hierarchical framework for contact prediction, with an application in membrane proteins. The hierarchical scheme consists of two levels: in the first level, contact residues are predicted from the sequence and their pairing relationships are further predicted in the second level. Statistical analyses on contact propensities are combined with other sequence and structural information for training the support vector machine classifiers. Evaluated on 52 protein chains using leave-one-out cross validation (LOOCV) and an independent test set of 14 protein chains, the two-level approach consistently improves the conventional direct approach in prediction accuracy, with 80% reduction of input for prediction. Furthermore, the predicted contacts are then used to infer interactions between pairs of helices. When at least three predicted contacts are required for an inferred interaction, the accuracy, sensitivity and specificity are 56%, 40% and 89%, respectively. Our results demonstrate that a hierarchical framework can be applied to eliminate false positives (FP) while reducing computational complexity in predicting contacts. Together with the estimated contact propensities, this method can be used to gain insights into helix-packing in membrane proteins. Availability: http://bio-cluster.iis.sinica.edu.tw/TMhit/ Contact: tsung@iis.sinica.edu.tw Supplementary information:Supplementary data are available at Bioinformatics online. PMID:19244388

Students' Understanding of Quadratic Equations

ERIC Educational Resources Information Center

López, Jonathan; Robles, Izraim; Martínez-Planell, Rafael

2016-01-01

Action-Process-Object-Schema theory (APOS) was applied to study student understanding of quadratic equations in one variable. This required proposing a detailed conjecture (called a genetic decomposition) of mental constructions students may do to understand quadratic equations. The genetic decomposition which was proposed can contribute to help…

Analytical approximations for the oscillators with anti-symmetric quadratic nonlinearity

NASA Astrophysics Data System (ADS)

Alal Hosen, Md.; Chowdhury, M. S. H.; Yeakub Ali, Mohammad; Faris Ismail, Ahmad

2017-12-01

A second-order ordinary differential equation involving anti-symmetric quadratic nonlinearity changes sign. The behaviour of the oscillators with an anti-symmetric quadratic nonlinearity is assumed to oscillate different in the positive and negative directions. In this reason, Harmonic Balance Method (HBM) cannot be directly applied. The main purpose of the present paper is to propose an analytical approximation technique based on the HBM for obtaining approximate angular frequencies and the corresponding periodic solutions of the oscillators with anti-symmetric quadratic nonlinearity. After applying HBM, a set of complicated nonlinear algebraic equations is found. Analytical approach is not always fruitful for solving such kinds of nonlinear algebraic equations. In this article, two small parameters are found, for which the power series solution produces desired results. Moreover, the amplitude-frequency relationship has also been determined in a novel analytical way. The presented technique gives excellent results as compared with the corresponding numerical results and is better than the existing ones.

Exact solutions to quadratic gravity

NASA Astrophysics Data System (ADS)

Pravda, V.; Pravdová, A.; Podolský, J.; Švarc, R.

2017-04-01

Since all Einstein spacetimes are vacuum solutions to quadratic gravity in four dimensions, in this paper we study various aspects of non-Einstein vacuum solutions to this theory. Most such known solutions are of traceless Ricci and Petrov type N with a constant Ricci scalar. Thus we assume the Ricci scalar to be constant which leads to a substantial simplification of the field equations. We prove that a vacuum solution to quadratic gravity with traceless Ricci tensor of type N and aligned Weyl tensor of any Petrov type is necessarily a Kundt spacetime. This will considerably simplify the search for new non-Einstein solutions. Similarly, a vacuum solution to quadratic gravity with traceless Ricci type III and aligned Weyl tensor of Petrov type II or more special is again necessarily a Kundt spacetime. Then we study the general role of conformal transformations in constructing vacuum solutions to quadratic gravity. We find that such solutions can be obtained by solving one nonlinear partial differential equation for a conformal factor on any Einstein spacetime or, more generally, on any background with vanishing Bach tensor. In particular, we show that all geometries conformal to Kundt are either Kundt or Robinson-Trautman, and we provide some explicit Kundt and Robinson-Trautman solutions to quadratic gravity by solving the above mentioned equation on certain Kundt backgrounds.

Pseudodynamic systems approach based on a quadratic approximation of update equations for diffuse optical tomography.

PubMed

Biswas, Samir Kumar; Kanhirodan, Rajan; Vasu, Ram Mohan; Roy, Debasish

2011-08-01

We explore a pseudodynamic form of the quadratic parameter update equation for diffuse optical tomographic reconstruction from noisy data. A few explicit and implicit strategies for obtaining the parameter updates via a semianalytical integration of the pseudodynamic equations are proposed. Despite the ill-posedness of the inverse problem associated with diffuse optical tomography, adoption of the quadratic update scheme combined with the pseudotime integration appears not only to yield higher convergence, but also a muted sensitivity to the regularization parameters, which include the pseudotime step size for integration. These observations are validated through reconstructions with both numerically generated and experimentally acquired data.

Competition for hydrogen-bond formation in the helix-coil transition and protein folding

NASA Astrophysics Data System (ADS)

Badasyan, A. V.; Tonoyan, Sh. A.; Mamasakhlisov, Y. Sh.; Giacometti, Achille; Benight, A. S.; Morozov, V. F.

2011-05-01

The problem of the helix-coil transition of biopolymers in explicit solvents, such as water, with the ability for hydrogen bonding with a solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide Chains. Besides the regular helix-coil transition, an additional coil-helix or reentrant transition is also found at lower temperatures. The reentrant transition arises due to competition between polymer-polymer and polymer-water hydrogen bonds. The balance between the two types of hydrogen bonding can be shifted to either direction through changes not only in temperature, but also by pressure, mechanical force, osmotic stress, or other external influences. Both polypeptides and polynucleotides are considered within a unified formalism. Our approach provides an explanation of the experimental difficulty of observing the reentrant transition with pressure and underscores the advantage of pulling experiments for studies of DNA. Results are discussed and compared with those reported in a number of recent publications with which a significant level of agreement is obtained.

Alternative C-Terminal Helix Orientation Alters Chemokine Function

PubMed Central

Kuo, Je-Hung; Chen, Ya-Ping; Liu, Jai-Shin; Dubrac, Alexandre; Quemener, Cathy; Prats, Hervé; Bikfalvi, Andreas; Wu, Wen-guey; Sue, Shih-Che

2013-01-01

Chemokines, a subfamily of cytokines, are small, secreted proteins that mediate a variety of biological processes. Various chemokines adopt remarkable conserved tertiary structure comprising an anti-parallel β-sheet core domain followed by a C-terminal helix that packs onto the β-sheet. The conserved structural feature has been considered critical for chemokine function, including binding to cell surface receptor. The recently isolated variant, CXCL4L1, is a homologue of CXCL4 chemokine (or platelet factor 4) with potent anti-angiogenic activity and differed only in three amino acid residues of P58L, K66E, and L67H. In this study we show by x-ray structural determination that CXCL4L1 adopts a previously unrecognized structure at its C terminus. The orientation of the C-terminal helix protrudes into the aqueous space to expose the entire helix. The alternative helix orientation modifies the overall chemokine shape and surface properties. The L67H mutation is mainly responsible for the swing-out effect of the helix, whereas mutations of P58L and K66E only act secondarily. This is the first observation that reports an open conformation of the C-terminal helix in a chemokine. This change leads to a decrease of its glycosaminoglycan binding properties and to an enhancement of its anti-angiogenic and anti-tumor effects. This unique structure is recent in evolution and has allowed CXCL4L1 to gain novel functional properties. PMID:23536183

Orthogonality preserving infinite dimensional quadratic stochastic operators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Akın, Hasan; Mukhamedov, Farrukh

In the present paper, we consider a notion of orthogonal preserving nonlinear operators. We introduce π-Volterra quadratic operators finite and infinite dimensional settings. It is proved that any orthogonal preserving quadratic operator on finite dimensional simplex is π-Volterra quadratic operator. In infinite dimensional setting, we describe all π-Volterra operators in terms orthogonal preserving operators.

Residue-Specific α-Helix Propensities from Molecular Simulation

PubMed Central

Best, Robert B.; de Sancho, David; Mittal, Jeetain

2012-01-01

Formation of α-helices is a fundamental process in protein folding and assembly. By studying helix formation in molecular simulations of a series of alanine-based peptides, we obtain the temperature-dependent α-helix propensities of all 20 naturally occurring residues with two recent additive force fields, Amber ff03w and Amber ff99SB∗. Encouragingly, we find that the overall helix propensity of many residues is captured well by both energy functions, with Amber ff99SB∗ being more accurate. Nonetheless, there are some residues that deviate considerably from experiment, which can be attributed to two aspects of the energy function: i), variations of the charge model used to determine the atomic partial charges, with residues whose backbone charges differ most from alanine tending to have the largest error; ii), side-chain torsion potentials, as illustrated by the effect of modifications to the torsion angles of I, L, D, N. We find that constrained refitting of residue charges for charged residues in Amber ff99SB∗ significantly improves their helix propensity. The resulting parameters should more faithfully reproduce helix propensities in simulations of protein folding and disordered proteins. PMID:22455930

Lipid solvation effects contribute to the affinity of Gly-xxx-Gly motif-mediated helix-helix interactions.

PubMed

Johnson, Rachel M; Rath, Arianna; Melnyk, Roman A; Deber, Charles M

2006-07-18

Interactions between transmembrane helices are mediated by the concave Gly-xxx-Gly motif surface. Whether Gly residues per se are sufficient for selection of this motif has not been established. Here, we used the in vivo TOXCAT assay to measure the relative affinities of all 18 combinations of Gly, Ala, and Ser "small-xxx-small" mutations in glycophorin A (GpA) and bacteriophage M13 major coat protein (MCP) homodimers. Affinity values were compared with the accessibility to a methylene-sized probe of the total surface area of each helix monomer as a measure of solvation by membrane components. A strong inverse correlation was found between nonpolar-group lipid accessibility and dimer affinity (R = 0.75 for GpA, p = 0.013, and R = 0.81 for MCP, p = 0.004), suggesting that lipid as a poor membrane protein solvent, conceptually analogous to water in soluble protein folding, can contribute to dimer stability and help to define helix-helix interfaces.

Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm

PubMed Central

Nugent, Timothy; Jones, David T.

2010-01-01

Alpha-helical transmembrane proteins constitute roughly 30% of a typical genome and are involved in a wide variety of important biological processes including cell signalling, transport of membrane-impermeable molecules and cell recognition. Despite significant efforts to predict transmembrane protein topology, comparatively little attention has been directed toward developing a method to pack the helices together. Here, we present a novel approach to predict lipid exposure, residue contacts, helix-helix interactions and finally the optimal helical packing arrangement of transmembrane proteins. Using molecular dynamics data, we have trained and cross-validated a support vector machine (SVM) classifier to predict per residue lipid exposure with 69% accuracy. This information is combined with additional features to train a second SVM to predict residue contacts which are then used to determine helix-helix interaction with up to 65% accuracy under stringent cross-validation on a non-redundant test set. Our method is also able to discriminate native from decoy helical packing arrangements with up to 70% accuracy. Finally, we employ a force-directed algorithm to construct the optimal helical packing arrangement which demonstrates success for proteins containing up to 13 transmembrane helices. This software is freely available as source code from http://bioinf.cs.ucl.ac.uk/memsat/mempack/. PMID:20333233

The CDRH helix. A phase I clinical trial.

PubMed

Shimm, D S; Cetas, T C; Hynynen, K H; Buechler, D N; Anhalt, D P; Sykes, H F; Cassady, J R

1989-04-01

Seventeen patients have been given regional hyperthermia treatments using the Center for Devices and Radiologic Health (CDRH) Helix, a resonant helical coil unit. Most of these patients had large, clinically advanced tumors, whose mean volume exceeded 1000 cc. Mean maximum, minimum, and average temperatures were 40.6, 38.6, and 39.6 degrees C, respectively, for all sites combined. The pelvic heating capabilities of the CDRH Helix and the BSD-1000 annular phased array were compared, and generally were equivalent. Although the Helix could be used in a wider variety of locations, and was more comfortable and easier to use than the BSD-1000 annular phased array, neither device was particularly effective in generating clinically useful temperatures; the Helix is currently under investigation for use in regional-systemic hyperthermia in combination with antineoplastic drugs and biologic response modifiers.

Kevlar: Transitioning Helix for Research to Practice

DTIC Science & Technology

2016-03-01

entropy randomization techniques, automated program repairs leveraging highly-optimized virtual machine technology, and developing a novel framework...attacker from exploiting residual vulnerabilities in a wide variety of classes. Helix/Kevlar uses novel, fine-grained, high- entropy diversification...the Air Force, and IARPA). Salient features of Helix/Kevlar include developing high- entropy randomization techniques, automated program repairs

Basic Helix-Loop-Helix Transcription Factor Gene Family Phylogenetics and Nomenclature

PubMed Central

Skinner, Michael K.; Rawls, Alan; Wilson-Rawls, Jeanne; Roalson, Eric H.

2010-01-01

A phylogenetic analysis of the basic helix-loop-helix (bHLH) gene superfamily was performed using seven different species (human, mouse, rat, worm, fly, yeast, and plant Arabidopsis) and involving over 600 bHLH genes [1]. All bHLH genes were identified in the genomes of the various species, including expressed sequence tags, and the entire coding sequence was used in the analysis. Nearly 15% of the gene family has been updated or added since the original publication. A super-tree involving six clades and all structural relationships was established and is now presented for four of the species. The wealth of functional data available for members of the bHLH gene superfamily provides us with the opportunity to use this exhaustive phylogenetic tree to predict potential functions of uncharacterized members of the family. This phylogenetic and genomic analysis of the bHLH gene family has revealed unique elements of the evolution and functional relationships of the different genes in the bHLH gene family. PMID:20219281

Frequency-independent approach to calculate physical optics radiations with the quadratic concave phase variations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Yu Mao, E-mail: yumaowu@fudan.edu.cn; Teng, Si Jia, E-mail: sjteng12@fudan.edu.cn

In this work, we develop the numerical steepest descent path (NSDP) method to calculate the physical optics (PO) radiations with the quadratic concave phase variations. With the surface integral equation method, the physical optics (PO) scattered fields are formulated and further reduced to the surface integrals. The high frequency physical critical points contributions, including the stationary phase points, the boundary resonance points and the vertex points are comprehensively studied via the proposed NSDP method. The key contributions of this work are twofold. One is that together with the PO integrals taking the quadratic parabolic and hyperbolic phase terms, this workmore » makes the NSDP theory be complete for treating the PO integrals with quadratic phase variations. Another is that, in order to illustrate the transition effect of the high frequency physical critical points, in this work, we consider and further extend the NSDP method to calculate the PO integrals with the coalescence of the high frequency critical points. Numerical results for the highly oscillatory PO integral with the coalescence of the critical points are given to verify the efficiency of the proposed NSDP method. The NSDP method could achieve the frequency independent computational workload and error controllable accuracy in all the numerical experiments, especially for the case of the coalescence of the high frequency critical points.« less

Interactions between the mixotrophic dinoflagellate Takayama helix and common heterotrophic protists.

PubMed

Ok, Jin Hee; Jeong, Hae Jin; Lim, An Suk; Lee, Kyung Ha

2017-09-01

The phototrophic dinoflagellate Takayama helix that is known to be harmful to abalone larvae has recently been revealed to be mixotrophic. Although mixotrophy elevates the growth rate of T. helix by 79%-185%, its absolute growth rate is still as low as 0.3d -1 . Thus, if the mortality rate of T. helix due to predation is high, this dinoflagellate may not easily prevail. To investigate potential effective protistan grazers on T. helix, feeding by diverse heterotrophic dinoflagellates such as engulfment-feeding Oxyrrhis marina, Gyrodinium dominans, Gyrodinium moestrupii, Polykrikos kofoidii, and Noctiluca scintillans, peduncle-feeding Aduncodinium glandula, Gyrodiniellum shiwhaense, Luciella masanensis, and Pfiesteria piscicida, pallium-feeding Oblea rotunda and Protoperidinium pellucidum, and the naked ciliates Pelagostrobilidium sp. (ca. 40μm in cell length) and Strombidinopsis sp. (ca. 150μm in cell length) on T. helix was explored. Among the tested heterotrophic protists, O. marina, G. dominans, G. moestrupii, A. glandula, L. masanensis, P. kofoidii, P. piscicida, and Strombidinopsis sp. were able to feed on T. helix. The growth rates of all these predators except Strombidinopsis sp. with T. helix prey were lower than those without the prey. The growth rate of Strombidinopsis sp. on T. helix was almost zero although the growth rate of Strombidinopsis sp. with T. helix prey was higher than those without the prey. Moreover, T. helix fed on O. marina and P. pellucidum and lysed the cells of P. kofoidii and G. shiwhaense. With increasing the concentrations of T. helix, the growth rates of O. marina and P. kofoidii decreased, but those of G. dominans and L. masanensis largely did not change. Therefore, reciprocal predation, lysis, no feeding, and the low ingestion rates of the common protists preying on T. helix may result in a low mortality rate due to predation, thereby compensating for this species' low growth rate. Copyright © 2017 Elsevier B.V. All rights

Position-dependent interactions between cysteine residues and the helix dipole

PubMed Central

Miranda, JJ L.

2003-01-01

A protein model was developed for studying the interaction between cysteine residues and the helix dipole. Site-directed mutagenesis was used to introduce cysteine residues at the N-terminus of helix H in recombinant sperm whale myoglobin. Based on the difference in thiol pKa between folded proteins and an unfolded peptide, the energy of interaction between the thiolate and the helix dipole was determined. Thiolates at the N1 and N2 positions of the helix were stabilized by 0.3 kcal/mole and 0.7 kcal/mole, respectively. A thiolate at the Ncap position was stabilized by 2.8 kcal/mole, and may involve a hydrogen bond. In context with other studies, an experimentally observed helix dipole effect may be defined in terms of two distinct components. A charge-dipole component involves electrostatic interactions with peptide bond dipoles in the first two turns of the helix and affects residues at all positions of the terminus; a hydrogen bond component involves one or more backbone amide groups and is only possible at the capping position due to conformational restraints elsewhere. The nature and magnitude of the helix dipole effect is, therefore, position-dependent. Results from this model system were used to interpret cysteine reactivity in rodent hemoglobins and the thioredoxin family. PMID:12493830

Robust Weak Chimeras in Oscillator Networks with Delayed Linear and Quadratic Interactions

NASA Astrophysics Data System (ADS)

Bick, Christian; Sebek, Michael; Kiss, István Z.

2017-10-01

We present an approach to generate chimera dynamics (localized frequency synchrony) in oscillator networks with two populations of (at least) two elements using a general method based on a delayed interaction with linear and quadratic terms. The coupling design yields robust chimeras through a phase-model-based design of the delay and the ratio of linear and quadratic components of the interactions. We demonstrate the method in the Brusselator model and experiments with electrochemical oscillators. The technique opens the way to directly bridge chimera dynamics in phase models and real-world oscillator networks.

Government and Governance of Regional Triple Helix Interactions

ERIC Educational Resources Information Center

Danson, Mike; Todeva, Emanuela

2016-01-01

This conceptual paper contributes to the discussion of the role of regional government and regional Triple Helix constellations driving economic development and growth within regional boundaries. The impact of regionalism and subsidiarity on regional Triple Helix constellations, and the questions of governmentality, governance and institutional…

A basic helix-loop-helix transcription factor, PhFBH4, regulates flower senescence by modulating ethylene biosynthesis pathway in petunia

USDA-ARS?s Scientific Manuscript database

The basic helix-loop-helix (bHLH) transcription factors (TFs) play important roles in regulating multiple biological processes in plants. However, there are few reports about the function of bHLHs in flower senescence. In this study, a bHLH TF, PhFBH4, was found to be dramatically upregulated during...

An α-Helix-Mimicking 12,13-Helix: Designed α/β/γ-Foldamers as Selective Inhibitors of Protein-Protein Interactions.

PubMed

Grison, Claire M; Miles, Jennifer A; Robin, Sylvie; Wilson, Andrew J; Aitken, David J

2016-09-05

A major current challenge in bioorganic chemistry is the identification of effective mimics of protein secondary structures that act as inhibitors of protein-protein interactions (PPIs). In this work, trans-2-aminocyclobutanecarboxylic acid (tACBC) was used as the key β-amino acid component in the design of α/β/γ-peptides to structurally mimic a native α-helix. Suitably functionalized α/β/γ-peptides assume an α-helix-mimicking 12,13-helix conformation in solution, exhibit enhanced proteolytic stability in comparison to the wild-type α-peptide parent sequence from which they are derived, and act as selective inhibitors of the p53/hDM2 interaction. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Identification of a basic helix-loop-helix-type transcription regulator gene in Aspergillus oryzae by systematically deleting large chromosomal segments.

PubMed

Jin, Feng Jie; Takahashi, Tadashi; Machida, Masayuki; Koyama, Yasuji

2009-09-01

We previously developed two methods (loop-out and replacement-type recombination) for generating large-scale chromosomal deletions that can be applied to more effective chromosomal engineering in Aspergillus oryzae. In this study, the replacement-type method is used to systematically delete large chromosomal DNA segments to identify essential and nonessential regions in chromosome 7 (2.93 Mb), which is the smallest A. oryzae chromosome and contains a large number of nonsyntenic blocks. We constructed 12 mutants harboring deletions that spanned 16- to 150-kb segments of chromosome 7 and scored phenotypic changes in the resulting mutants. Among the deletion mutants, strains designated Delta5 and Delta7 displayed clear phenotypic changes involving growth and conidiation. In particular, the Delta5 mutant exhibited vigorous growth and conidiation, potentially beneficial characteristics for certain industrial applications. Further deletion analysis allowed identification of the AO090011000215 gene as the gene responsible for the Delta5 mutant phenotype. The AO090011000215 gene was predicted to encode a helix-loop-helix binding protein belonging to the bHLH family of transcription factors. These results illustrate the potential of the approach for identifying novel functional genes.

A directional nucleation-zipping mechanism for triple helix formation

PubMed Central

Alberti, Patrizia; Arimondo, Paola B.; Mergny, Jean-Louis; Garestier, Thérèse; Hélène, Claude; Sun, Jian-Sheng

2002-01-01

A detailed kinetic study of triple helix formation was performed by surface plasmon resonance. Three systems were investigated involving 15mer pyrimidine oligonucleotides as third strands. Rate constants and activation energies were validated by comparison with thermodynamic values calculated from UV-melting analysis. Replacement of a T·A base pair by a C·G pair at either the 5′ or the 3′ end of the target sequence allowed us to assess mismatch effects and to delineate the mechanism of triple helix formation. Our data show that the association rate constant is governed by the sequence of base triplets on the 5′ side of the triplex (referred to as the 5′ side of the target oligopurine strand) and provides evidence that the reaction pathway for triple helix formation in the pyrimidine motif proceeds from the 5′ end to the 3′ end of the triplex according to the nucleation-zipping model. It seems that this is a general feature for all triple helices formation, probably due to the right-handedness of the DNA double helix that provides a stronger base stacking at the 5′ than at the 3′ duplex–triplex junction. Understanding the mechanism of triple helix formation is not only of fundamental interest, but may also help in designing better triple helix-forming oligonucleotides for gene targeting and control of gene expression. PMID:12490709

Effect of Hedera helix on lung histopathology in chronic asthma.

PubMed

Hocaoglu, Arzu Babayigit; Karaman, Ozkan; Erge, Duygu Olmez; Erbil, Guven; Yilmaz, Osman; Kivcak, Bijen; Bagriyanik, H Alper; Uzuner, Nevin

2012-12-01

Hedera helix is widely used to treat bronchial asthma for many years. However, effects of this herb on lung histopathology is still far from clear. We aimed to determine the effect of oral administration of Hedera helix on lung histopathology in a murine model of chronic asthma.BALB/c mice were divided into four groups; I (Placebo), II (Hedera helix), III (Dexamethasone) and IV (Control). All mice except controls were sensitized and challenged with ovalbumin. Then, mice in group I received saline, group II 100 mg/kg Hedera helix and group III 1 mg/kg dexamethasone via orogastic gavage once daily for one week. Airway histopathology was evaluated by using light and electron microscopy in all groups.Goblet cell numbers and thicknesses of basement membrane were found significantly lower in group II, but there was no statistically significant difference in terms of number of mast cells, thicknesses of epithelium and subepithelial smooth muscle layers between group I and II. When Hedera helix and dexamethasone groups were compared with each other, thickness of epithelium, subepithelial muscle layers, number of mast cells and goblet cells of group III were significantly ameliorated when compared with the group II. Although Hedera helix administration reduced only goblet cell counts and the thicknesses of basement membrane in the asthmatic airways, dexamethasone ameliorated all histopathologic parameters except thickness of basement membrane better than Hedera helix.

Dimerization of the docking/adaptor protein HEF1 via a carboxy-terminal helix-loop-helix domain.

PubMed

Law, S F; Zhang, Y Z; Fashena, S J; Toby, G; Estojak, J; Golemis, E A

1999-10-10

HEF1, p130(Cas), and Efs define a family of multidomain docking proteins which plays a central coordinating role for tyrosine-kinase-based signaling related to cell adhesion. HEF1 function has been specifically implicated in signaling pathways important for cell adhesion and differentiation in lymphoid and epithelial cells. While the SH3 domains and SH2-binding site domains (substrate domains) of HEF1 family proteins are well characterized and binding partners known, to date the highly conserved carboxy-terminal domains of the three proteins have lacked functional definition. In this study, we have determined that the carboxy-terminal domain of HEF1 contains a divergent helix-loop-helix (HLH) motif. This motif mediates HEF1 homodimerization and HEF1 heterodimerization with a recognition specificity similar to that of the transcriptional regulatory HLH proteins Id2, E12, and E47. We had previously demonstrated that the HEF1 carboxy-terminus expressed as a separate domain in yeast reprograms cell division patterns, inducing constitutive pseudohyphal growth. Here we show that pseudohyphal induction by HEF1 requires an intact HLH, further supporting the idea that this motif has an effector activity for HEF1, and implying that HEF1 pseudohyphal activity derives in part from interactions with yeast helix-loop-helix proteins. These combined results provide initial insight into the mode of function of the HEF1 carboxy-terminal domain and suggest that the HEF1 protein may interact with cellular proteins which control differentiation. Copyright 1999 Academic Press.

Triple Helix

DTIC Science & Technology

2008-08-01

and sponsoring FIRST teams at the Junior FIRST Lego League (JFLL) and the FIRST Lego League (FLL) levels in elementary and middle school . As such, the...a Final Technical Report for Year I Grant W911NF-07-1-0663 with the Newport News Public School District for the Menchville High School Robotics Team...August 2008 TRIPL HELIX 0 Menchville High School Newport News, VA 20080829081 w DEFENSE TECHNICAL INFORMATION CENTER bfro do.A icfr tkw, Def&*ue, Cow

An Unexpected Influence on a Quadratic

ERIC Educational Resources Information Center

Davis, Jon D.

2013-01-01

Using technology to explore the coefficients of a quadratic equation can lead to an unexpected result. This article describes an investigation that involves sliders and dynamically linked representations. It guides students to notice the effect that the parameter "a" has on the graphical representation of a quadratic function in the form…

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system.

PubMed

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

2015-11-19

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database in which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. This database will facilitate the analysis of protein-DNA interactions and the development of

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

DOE Office of Scientific and Technical Information (OSTI.GOV)

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database inmore » which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

DOE PAGES

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

2015-11-19

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database inmore » which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the

Evaluation of Doxorubicin-loaded 3-Helix Micelles as Nanocarriers

PubMed Central

Dube, Nikhil; Shu, Jessica Y.; Dong, He; Seo, Jai W.; Ingham, Elizabeth; Kheirolomoom, Azadeh; Chen, Pin-Yuan; Forsayeth, John; Bankiewicz, Krystof; Ferrara, Katherine W.; Xu, Ting

2013-01-01

Designing stable drug nanocarriers, 10-30 nm in size, would have significant impact on their transport in circulation, tumor penetration and therapeutic efficacy. In the present study, biological properties of 3-helix micelles loaded with 8 wt% doxorubicin (DOX), ~15 nm in size, were characterized to validate their potential as a nanocarrier platform. DOX-loaded micelles exhibited high stability in terms of size and drug retention in concentrated protein environments similar to conditions after intravenous injections. DOX-loaded micelles were cytotoxic to PPC-1 and 4T1 cancer cells at levels comparable to free DOX. 3-helix micelles can be disassembled by proteolytic degradation of peptide shell to enable drug release and clearance to minimize long-term accumulation. Local administration to normal rat striatum by convection enhanced delivery (CED) showed greater extent of drug distribution and reduced toxicity relative to free drug. Intravenous administration of DOX-loaded 3-helix micelles demonstrated improved tumor half-life and reduced toxicity to healthy tissues in comparison to free DOX. In vivo delivery of DOX-loaded 3-helix micelles through two different routes clearly indicates the potential of 3-helix micelles as safe and effective nanocarriers for cancer therapeutics. PMID:24050265

Cytotoxic Helix-Rich Oligomer Formation by Melittin and Pancreatic Polypeptide

PubMed Central

Singh, Pradeep K.; Ghosh, Dhiman; Tewari, Debanjan; Mohite, Ganesh M.; Carvalho, Edmund; Jha, Narendra Nath; Jacob, Reeba S.; Sahay, Shruti; Banerjee, Rinti; Bera, Amal K.; Maji, Samir K.

2015-01-01

Conversion of amyloid fibrils by many peptides/proteins involves cytotoxic helix-rich oligomers. However, their toxicity and biophysical studies remain largely unknown due to their highly dynamic nature. To address this, we chose two helical peptides (melittin, Mel and pancreatic polypeptide, PP) and studied their aggregation and toxicity. Mel converted its random coil structure to oligomeric helical structure upon binding to heparin; however, PP remained as helix after oligomerization. Interestingly, similar to Parkinson’s associated α-synuclein (AS) oligomers, Mel and PP also showed tinctorial properties, higher hydrophobic surface exposure, cellular toxicity and membrane pore formation after oligomerization in the presence of heparin. We suggest that helix-rich oligomers with exposed hydrophobic surface are highly cytotoxic to cells irrespective of their disease association. Moreover as Mel and PP (in the presence of heparin) instantly self-assemble into stable helix-rich amyloidogenic oligomers; they could be represented as models for understanding the biophysical and cytotoxic properties of helix-rich intermediates in detail. PMID:25803428

Quadrifilar Helix Antenna for Enhanced Air-to-Ground Communications

DTIC Science & Technology

2016-05-01

ARL-TR-7679 ● MAY 2016 US Army Research Laboratory Quadrifilar Helix Antenna for Enhanced Air-to- Ground Communications by...Research Laboratory Quadrifilar Helix Antenna for Enhanced Air-to- Ground Communications by Steven D Keller, William O Coburn, Theodore K Anthony...

A Comparison of Methods for Estimating Quadratic Effects in Nonlinear Structural Equation Models

ERIC Educational Resources Information Center

Harring, Jeffrey R.; Weiss, Brandi A.; Hsu, Jui-Chen

2012-01-01

Two Monte Carlo simulations were performed to compare methods for estimating and testing hypotheses of quadratic effects in latent variable regression models. The methods considered in the current study were (a) a 2-stage moderated regression approach using latent variable scores, (b) an unconstrained product indicator approach, (c) a latent…

Seven Wonders of the Ancient and Modern Quadratic World.

ERIC Educational Resources Information Center

Taylor, Sharon E.; Mittag, Kathleen Cage

2001-01-01

Presents four methods for solving a quadratic equation using graphing calculator technology: (1) graphing with the CALC feature; (2) quadratic formula program; (3) table; and (4) solver. Includes a worksheet for a lab activity on factoring quadratic equations. (KHR)

OVERVIEW OF HELIX HOUSE NO. 2 (S87), WITH ANTENNA TOWERS, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

OVERVIEW OF HELIX HOUSE NO. 2 (S-87), WITH ANTENNA TOWERS, HELIX HOUSE NO. 1 (S-3) AND TRANSMITTER BLDG. (S-2) AT REAR, LOOKING WEST SOUTHWEST. - Naval Computer & Telecommunications Area Master Station, Eastern Pacific, Radio Transmitter Facility Lualualei, Helix House No. 2, Base of Radio Antenna Structure No. 427, Makaha, Honolulu County, HI

Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin

PubMed Central

2018-01-01

Mechanical stability is a key feature in the regulation of structural scaffolding proteins and their functions. Despite the abundance of α-helical structures among the human proteome and their undisputed importance in health and disease, the fundamental principles of their behavior under mechanical load are poorly understood. Talin and α-catenin are two key molecules in focal adhesions and adherens junctions, respectively. In this study, we used a combination of atomistic steered molecular dynamics (SMD) simulations, polyprotein engineering, and single-molecule atomic force microscopy (smAFM) to investigate unfolding of these proteins. SMD simulations revealed that talin rod α-helix bundles as well as α-catenin α-helix domains unfold through stable 3-helix intermediates. While the 5-helix bundles were found to be mechanically stable, a second stable conformation corresponding to the 3-helix state was revealed. Mechanically weaker 4-helix bundles easily unfolded into a stable 3-helix conformation. The results of smAFM experiments were in agreement with the findings of the computational simulations. The disulfide clamp mutants, designed to protect the stable state, support the 3-helix intermediate model in both experimental and computational setups. As a result, multiple discrete unfolding intermediate states in the talin and α-catenin unfolding pathway were discovered. Better understanding of the mechanical unfolding mechanism of α-helix proteins is a key step towards comprehensive models describing the mechanoregulation of proteins. PMID:29698481

THE EFFECTIVENESS OF QUADRATS FOR MEASURING VASCULAR PLANT DIVERSITY

EPA Science Inventory

Quadrats are widely used for measuring characteristics of vascular plant communities. It is well recognized that quadrat size affects measurements of frequency and cover. The ability of quadrats of varying sizes to adequately measure diversity has not been established. An exha...

Thermodynamics of the pseudo-knot in helix 18 of 16S ribosomal RNA.

PubMed

Wojciechowska, Monika; Dudek, Marta; Trylska, Joanna

2018-04-01

A fragment of E. coli 16S rRNA formed by nucleotides 500 to 545 is termed helix 18. Nucleotides 505-507 and 524-526 form a pseudo-knot and its distortion affects ribosome function. Helix 18 isolated from the ribosome context is thus an interesting fragment to investigate the structural properties and folding of RNA with pseudo-knots. With all-atom molecular dynamics simulations, spectroscopic and gel electrophoresis experiments, we investigated thermodynamics of helix 18, with a focus on its pseudo-knot. In solution studies at ambient conditions we observed dimerization of helix 18. We proposed that the loop, containing nucleotides forming the pseudo-knot, interacts with another monomer of helix 18. The native dimer is difficult to break but introducing mutations in the pseudo-knot indeed assured a monomeric form of helix 18. Molecular dynamics simulations at 310 K confirmed the stability of the pseudo-knot but at elevated temperatures this pseudo-knot was the first part of helix 18 to lose the hydrogen bond pattern. To further determine helix 18 stability, we analyzed the interactions of helix 18 with short oligomers complementary to a nucleotide stretch containing the pseudo-knot. The formation of higher-order structures by helix 18 impacts hybridization efficiency of peptide nucleic acid and 2'-O methyl RNA oligomers. © 2018 Wiley Periodicals, Inc.

The role of alpha-, 3(10)-, and pi-helix in helix-->coil transitions.

PubMed

Armen, Roger; Alonso, Darwin O V; Daggett, Valerie

2003-06-01

The conformational equilibrium between 3(10)- and alpha-helical structure has been studied via high-resolution NMR spectroscopy by Millhauser and coworkers using the MW peptide Ac-AMAAKAWAAKA AAARA-NH2. Their 750-MHz nuclear Overhauser effect spectroscopy (NOESY) spectra were interpreted to reflect appreciable populations of 3(10)-helix throughout the peptide, with the greatest contribution at the N and C termini. The presence of simultaneous alphaN(i,i + 2) and alphaN(i,i + 4) NOE cross-peaks was proposed to represent conformational averaging between 3(10)- and alpha-helical structures. In this study, we describe 25-nsec molecular dynamics simulations of the MW peptide at 298 K, using both an 8 A and a 10 A force-shifted nonbonded cutoff. The ensemble averages of both simulations are in reasonable agreement with the experimental helical content from circular dichroism (CD), the (3)J(HNalpha) coupling constants, and the 57 observed NOEs. Analysis of the structures from both simulations revealed very little formation of contiguous i --> i + 3 hydrogen bonds (3(10)-helix); however, there was a large population of bifurcated i --> i + 3 and i --> i + 4 alpha-helical hydrogen bonds. In addition, both simulations contained considerable populations of pi-helix (i --> i + 5 hydrogen bonds). Individual turns formed over residues 1-9, which we predict contribute to the intensities of the experimentally observed alphaN(i,i + 2) NOEs. Here we show how sampling of both folded and unfolded structures can provide a structural framework for deconvolution of the conformational contributions to experimental ensemble averages.

Planetary Nebula NGC 7293 also Known as the Helix Nebula

NASA Image and Video Library

2005-05-05

This ultraviolet image from NASA Galaxy Evolution Explorer is of the planetary nebula NGC 7293 also known as the Helix Nebula. It is the nearest example of what happens to a star, like our own Sun, as it approaches the end of its life when it runs out of fuel, expels gas outward and evolves into a much hotter, smaller and denser white dwarf star. http://photojournal.jpl.nasa.gov/catalog/PIA07902

Hexa Helix: Modified Quad Helix Appliance to Correct Anterior and Posterior Crossbites in Mixed Dentition

PubMed Central

Yaseen, Syed Mohammed; Acharya, Ravindranath

2012-01-01

Among the commonly encountered dental irregularities which constitute developing malocclusion is the crossbite. During primary and mixed dentition phase, the crossbite is seen very often and if left untreated during these phases then a simple problem may be transformed into a more complex problem. Different techniques have been used to correct anterior and posterior crossbites in mixed dentition. This case report describes the use of hexa helix, a modified version of quad helix for the management of anterior crossbite and bilateral posterior crossbite in early mixed dentition. Correction was achieved within 15 weeks with no damage to the tooth or the marginal periodontal tissue. The procedure is a simple and effective method for treating anterior and bilateral posterior crossbites simultaneously. PMID:23119188

Salt- and pH-Triggered Helix-Coil Transition of Ionic Polypeptides under Physiology Conditions.

PubMed

Yuan, Jingsong; Zhang, Yi; Sun, Yue; Cai, Zhicheng; Yang, Lijiang; Lu, Hua

2018-06-11

Controlling the helix-coil transition of polypeptides under physiological conditions is an attractive way toward smart functional materials. Here, we report the synthesis of a series of tertiary amine-functionalized ethylene glycol (EG x )-linked polypeptide electrolytes with their secondary structures tunable under physiological conditions. The resultant polymers, denoted as P(EG x DMA-Glu) ( x = 1, 2, and 3), show excellent aqueous solubility (>20 mg/mL) regardless of their charge states. Unlike poly-l-lysine that can form a helix only at pH above 10, P(EG x DMA-Glu) undergo a pH-dependent helix-coil switch with their transition points within the physiological range (pH ∼5.3-6.5). Meanwhile, P(EG x DMA-Glu) exhibit an unusual salt-induced helical conformation presumably owing to the unique properties of EG x linkers. Together, the current work highlights the importance of fine-tuning the linker chemistry in achieving conformation-switchable polypeptides and represents a facile approach toward stimuli-responsive biopolymers for advanced biological applications.

Design of reinforced areas of concrete column using quadratic polynomials

NASA Astrophysics Data System (ADS)

Arif Gunadi, Tjiang; Parung, Herman; Rachman Djamaluddin, Abd; Arwin Amiruddin, A.

2017-11-01

Designing of reinforced concrete columns mostly carried out by a simple planning method which uses column interaction diagram. However, the application of this method is limited because it valids only for certain compressive strenght of the concrete and yield strength of the reinforcement. Thus, a more applicable method is still in need. Another method is the use of quadratic polynomials as a basis for the approach in designing reinforced concrete columns, where the ratio of neutral lines to the effective height of a cross section (ξ) if associated with ξ in the same cross-section with different reinforcement ratios is assumed to form a quadratic polynomial. This is identical to the basic principle used in the Simpson rule for numerical integral using quadratic polynomials and had a sufficiently accurate level of accuracy. The basis of this approach to be used both the normal force equilibrium and the moment equilibrium. The abscissa of the intersection of the two curves is the ratio that had been mentioned, since it fulfill both of the equilibrium. The application of this method is relatively more complicated than the existing method but provided with tables and graphs (N vs ξN ) and (M vs ξM ) so that its used could be simplified. The uniqueness of these tables are only distinguished based on the compresssive strength of the concrete, so in application it could be combined with various yield strenght of the reinforcement available in the market. This method could be solved by using programming languages such as Fortran.

Towards a unifying approach to diversity measures: bridging the gap between the Shannon entropy and Rao's quadratic index.

PubMed

Ricotta, Carlo; Szeidl, Laszlo

2006-11-01

The diversity of a species assemblage has been studied extensively for many decades in relation to its possible connection with ecosystem functioning and organization. In this view most diversity measures, such as Shannon's entropy, rely upon information theory as a basis for the quantification of diversity. Also, traditional diversity measures are computed using species relative abundances and cannot account for the ecological differences between species. Rao first proposed a diversity index, termed quadratic diversity (Q) that incorporates both species relative abundances and pairwise distances between species. Quadratic diversity is traditionally defined as the expected distance between two randomly selected individuals. In this paper, we show that quadratic diversity can be interpreted as the expected conflict among the species of a given assemblage. From this unusual interpretation, it naturally follows that Rao's Q can be related to the Shannon entropy through a generalized version of the Tsallis parametric entropy.

Control of Transmembrane Helix Dynamics by Interfacial Tryptophan Residues.

PubMed

McKay, Matthew J; Martfeld, Ashley N; De Angelis, Anna A; Opella, Stanley J; Greathouse, Denise V; Koeppe, Roger E

2018-06-05

Transmembrane protein domains often contain interfacial aromatic residues, which may play a role in the insertion and stability of membrane helices. Residues such as Trp or Tyr, therefore, are often found situated at the lipid-water interface. We have examined the extent to which the precise radial locations of interfacial Trp residues may influence peptide helix orientation and dynamics. To address these questions, we have modified the GW 5,19 ALP23 (acetyl-GGALW 5 (LA) 6 LW 19 LAGA-[ethanol]amide) model peptide framework to relocate the Trp residues. Peptide orientation and dynamics were analyzed by means of solid-state nuclear magnetic resonance (NMR) spectroscopy to monitor specific 2 H- and 15 N-labeled residues. GW 5,19 ALP23 adopts a defined, tilted orientation within lipid bilayer membranes with minimal evidence of motional averaging of NMR observables, such as 2 H quadrupolar or 15 N- 1 H dipolar splittings. Here, we examine how peptide dynamics are impacted by relocating the interfacial Trp (W) residues on both ends and opposing faces of the helix, for example by a 100° rotation on the helical wheel for positions 4 and 20. In contrast to GW 5,19 ALP23, the modified GW 4,20 ALP23 helix experiences more extensive motional averaging of the NMR observables in several lipid bilayers of different thickness. Individual and combined Gaussian analyses of the 2 H and 15 N NMR signals confirm that the extent of dynamic averaging, particularly rotational "slippage" about the helix axis, is strongly coupled to the radial distribution of the interfacial Trp residues as well as the bilayer thickness. Additional 2 H labels on alanines A3 and A21 reveal partial fraying of the helix ends. Even within the context of partial unwinding, the locations of particular Trp residues around the helix axis are prominent factors for determining transmembrane helix orientation and dynamics within the lipid membrane environment. Copyright © 2018 Biophysical Society. Published by

Hydroxyproline Ring Pucker Causes Frustration of Helix Parameters in the Collagen Triple Helix

NASA Astrophysics Data System (ADS)

Ying Chow, W.; Bihan, Dominique; Forman, Chris J.; Slatter, David A.; Reid, David G.; Wales, David J.; Farndale, Richard W.; Duer, Melinda J.

2015-07-01

Collagens, the most abundant proteins in mammals, are defined by their triple-helical structures and distinctive Gly-Xaa-Yaa repeating sequence, where Xaa is often proline and Yaa, hydroxyproline (Hyp/O). It is known that hydroxyproline in the Yaa position stabilises the triple helix, and that lack of proline hydroxylation in vivo leads to dysfunctional collagen extracellular matrix assembly, due to a range of factors such as a change in hydration properties. In addition, we note that in model peptides, when Yaa is unmodified proline, the Xaa proline has a strong propensity to adopt an endo ring conformation, whilst when Yaa is hydroxyproline, the Xaa proline adopts a range of endo and exo conformations. Here we use a combination of solid-state NMR spectroscopy and potential energy landscape modelling of synthetic triple-helical collagen peptides to understand this effect. We show that hydroxylation of the Yaa proline causes the Xaa proline ring conformation to become metastable, which in turn confers flexibility on the triple helix.

Hydroxyproline Ring Pucker Causes Frustration of Helix Parameters in the Collagen Triple Helix

PubMed Central

Ying Chow, W.; Bihan, Dominique; Forman, Chris J.; Slatter, David A.; Reid, David G.; Wales, David J.; Farndale, Richard W.; Duer, Melinda J.

2015-01-01

Collagens, the most abundant proteins in mammals, are defined by their triple-helical structures and distinctive Gly-Xaa-Yaa repeating sequence, where Xaa is often proline and Yaa, hydroxyproline (Hyp/O). It is known that hydroxyproline in the Yaa position stabilises the triple helix, and that lack of proline hydroxylation in vivo leads to dysfunctional collagen extracellular matrix assembly, due to a range of factors such as a change in hydration properties. In addition, we note that in model peptides, when Yaa is unmodified proline, the Xaa proline has a strong propensity to adopt an endo ring conformation, whilst when Yaa is hydroxyproline, the Xaa proline adopts a range of endo and exo conformations. Here we use a combination of solid-state NMR spectroscopy and potential energy landscape modelling of synthetic triple-helical collagen peptides to understand this effect. We show that hydroxylation of the Yaa proline causes the Xaa proline ring conformation to become metastable, which in turn confers flexibility on the triple helix. PMID:26220399

Local hyperspectral data multisharpening based on linear/linear-quadratic nonnegative matrix factorization by integrating lidar data

NASA Astrophysics Data System (ADS)

Benhalouche, Fatima Zohra; Karoui, Moussa Sofiane; Deville, Yannick; Ouamri, Abdelaziz

2015-10-01

In this paper, a new Spectral-Unmixing-based approach, using Nonnegative Matrix Factorization (NMF), is proposed to locally multi-sharpen hyperspectral data by integrating a Digital Surface Model (DSM) obtained from LIDAR data. In this new approach, the nature of the local mixing model is detected by using the local variance of the object elevations. The hyper/multispectral images are explored using small zones. In each zone, the variance of the object elevations is calculated from the DSM data in this zone. This variance is compared to a threshold value and the adequate linear/linearquadratic spectral unmixing technique is used in the considered zone to independently unmix hyperspectral and multispectral data, using an adequate linear/linear-quadratic NMF-based approach. The obtained spectral and spatial information thus respectively extracted from the hyper/multispectral images are then recombined in the considered zone, according to the selected mixing model. Experiments based on synthetic hyper/multispectral data are carried out to evaluate the performance of the proposed multi-sharpening approach and literature linear/linear-quadratic approaches used on the whole hyper/multispectral data. In these experiments, real DSM data are used to generate synthetic data containing linear and linear-quadratic mixed pixel zones. The DSM data are also used for locally detecting the nature of the mixing model in the proposed approach. Globally, the proposed approach yields good spatial and spectral fidelities for the multi-sharpened data and significantly outperforms the used literature methods.

Topological distribution of four-alpha-helix bundles.

PubMed Central

Presnell, S R; Cohen, F E

1989-01-01

The four-alpha-helix bundle, a common structural motif in globular proteins, provides an excellent forum for the examination of predictive constraints for protein backbone topology. An exhaustive examination of the Brookhaven Crystallographic Protein Data Bank and other literature sources has lead to the discovery of 20 putative four-alpha-helix bundles. Application of an analytical method that examines the difference between solvent-accessible surface areas in packed and partially unpacked bundles reduced the number of structures to 16. Angular requirements further reduced the list of bundles to 13. In 12 of these bundles, all pairs of neighboring helices were oriented in an anti-parallel fashion. This distribution is in accordance with structure types expected if the helix macro dipole effect makes a substantial contribution to the stability of the native structure. The characterizations and classifications made in this study prompt a reevaluation of constraints used in structure prediction efforts. Images PMID:2771946

Nature of the Charged-Group Effect on the Stability of the C-Peptide Helix

NASA Astrophysics Data System (ADS)

Shoemaker, Kevin R.; Kim, Peter S.; Brems, David N.; Marqusee, Susan; York, Eunice J.; Chaiken, Irwin M.; Stewart, John M.; Baldwin, Robert L.

1985-04-01

The residues responsible for the pH-dependent stability of the helix formed by the isolated C-peptide (residues 1-13 of ribonuclease A) have been identified by chemical synthesis of analogues and measurement of their helix-forming properties. Each of the residues ionizing between pH 2 and pH 8 has been replaced separately by an uncharged residue. Protonation of Glu-2- is responsible for the sharp decrease in helix stability between pH 5 and pH 2, and deprotonation of His-12+ causes a similar decrease between pH 5 and pH 8. Glu-9- is not needed for helix stability. The results cannot be explained by the Zimm-Bragg model and host-guest data for α -helix formation, which predict that the stability of the C-peptide helix should increase when Glu-2- is protonated or when His-12+ is deprotonated. Moreover, histidine+ is a strong helix-breaker in host-guest studies. In proteins, acidic and basic residues tend to occur at opposite ends of α -helices: acidic residues occur preferentially near the NH2-terminal end and basic residues near the COOH-terminal end. A possible explanation, based on a helix dipole model, has been given [Blagdon, D. E. & Goodman, M. (1975) Biopolymers 14, 241-245]. Our results are consistent with the helix dipole model and they support the suggestion that the distribution of charged residues in protein helices reflects the helix-stabilizing propensity of those residues. Because Glu-9 is not needed for helix stability, a possible Glu-9-\\cdots His-12+ salt bridge does not contribute significantly to helix stability. The role of a possible Glu-2-\\cdots Arg-10+ salt bridge has not yet been evaluated. A charged-group effect on α -helix stability in water has also been observed in a different peptide system [Ihara, S., Ooi, T. & Takahashi, S. (1982) Biopolymers 21, 131-145]: block copolymers containing (Ala)20 and (Glu)20 show partial helix formation at low temperatures, pH 7.5, where the glutamic acid residues are ionized. (Glu)20(Ala)20Phe forms a

Magneto-chiral anisotropy of the free electron on a helix

NASA Astrophysics Data System (ADS)

Krstić, V.; Rikken, G. L. J. A.

2002-09-01

The free electron on a helix as a simple model of a molecular chiral conductor is considered. In the presence of a static magnetic field parallel to the helix axis, it is found that both ballistic and diffusive electrical transport along the helix show a conductivity that depends linearly on the current and the magnetic field and on the handedness of the helix. These results agree qualitatively with the recently experimentally observed electrical magneto-chiral anisotropy in carbon nanotubes [V. Krstić, S. Roth, M. Burghard, K. Kern, G.L.J.A. Rikken, Max-Planck-Institut für Festkörperforschung, Stuttgart, Germany; Grenoble High Magnetic Field Laboratory, MPI-CNRS, Grenoble, France; Laboratoire National des Champs Magnétiques Pulsés, CNRS/INSA/UPS, UMS 5462, Toulouse, France].

An iterative method for tri-level quadratic fractional programming problems using fuzzy goal programming approach

NASA Astrophysics Data System (ADS)

Kassa, Semu Mitiku; Tsegay, Teklay Hailay

2017-08-01

Tri-level optimization problems are optimization problems with three nested hierarchical structures, where in most cases conflicting objectives are set at each level of hierarchy. Such problems are common in management, engineering designs and in decision making situations in general, and are known to be strongly NP-hard. Existing solution methods lack universality in solving these types of problems. In this paper, we investigate a tri-level programming problem with quadratic fractional objective functions at each of the three levels. A solution algorithm has been proposed by applying fuzzy goal programming approach and by reformulating the fractional constraints to equivalent but non-fractional non-linear constraints. Based on the transformed formulation, an iterative procedure is developed that can yield a satisfactory solution to the tri-level problem. The numerical results on various illustrative examples demonstrated that the proposed algorithm is very much promising and it can also be used to solve larger-sized as well as n-level problems of similar structure.

"Special Issue": Regional Dimensions of the Triple Helix Model

ERIC Educational Resources Information Center

Todeva, Emanuela; Danson, Mike

2016-01-01

This paper introduces the rationale for the special issue and its contributions, which bridge the literature on regional development and the Triple Helix model. The concept of the Triple Helix at the sub-national, and specifically regional, level is established and examined, with special regard to regional economic development founded on…

The algebraic decoding of the (41, 21, 9) quadratic residue code

NASA Technical Reports Server (NTRS)

Reed, Irving S.; Truong, T. K.; Chen, Xuemin; Yin, Xiaowei

1992-01-01

A new algebraic approach for decoding the quadratic residue (QR) codes, in particular the (41, 21, 9) QR code is presented. The key ideas behind this decoding technique are a systematic application of the Sylvester resultant method to the Newton identities associated with the code syndromes to find the error-locator polynomial, and next a method for determining error locations by solving certain quadratic, cubic and quartic equations over GF(2 exp m) in a new way which uses Zech's logarithms for the arithmetic. The algorithms developed here are suitable for implementation in a programmable microprocessor or special-purpose VLSI chip. It is expected that the algebraic methods developed here can apply generally to other codes such as the BCH and Reed-Solomon codes.

The Other Double Helix--The Fascinating Chemistry of Starch

NASA Astrophysics Data System (ADS)

Hancock, Robert D.; Tarbet, Bryon J.

2000-08-01

Current textbooks deal only briefly with the chemistry of starch. A short review with 21 references is presented, describing the structure of starch and indicating the double helix structure of A-type and B-type starch. The structure of the starch granule is examined, pointing out the existence of growth rings of alternating crystalline and noncrystalline starch, with growing amylopectin molecules extending from the hilum (point of origin) to the surface of the starch granule. The swelling of starch granules in water, above the gelatinization temperature of about 60 °C, is discussed. The process of gelatinization involves unraveling of the starch helix and a manyfold increase in volume of the starch granule as water is imbibed and bound to the unraveled starch polymer by hydrogen bonding. Baking bread or pastries causes unraveling of the starch helix, and the process by which these products become stale corresponds primarily to the re-forming of the starch helix. The importance of this phenomenon in food science is discussed. The absorption of nonpolar linear molecules such as I2, or linear nonpolar portions of molecules such as n-butanol or fats and phospholipids, by the C-type helix of starch is examined. The way in which starch is structurally modified to retard staling is discussed in relation to food technology.

On the time-weighted quadratic sum of linear discrete systems

NASA Technical Reports Server (NTRS)

Jury, E. I.; Gutman, S.

1975-01-01

A method is proposed for obtaining the time-weighted quadratic sum for linear discrete systems. The formula of the weighted quadratic sum is obtained from matrix z-transform formulation. In addition, it is shown that this quadratic sum can be derived in a recursive form for several useful weighted functions. The discussion presented parallels that of MacFarlane (1963) for weighted quadratic integral for linear continuous systems.

Data on diverse roles of helix perturbations in membrane proteins.

PubMed

Shelar, Ashish; Bansal, Manju

2016-12-01

The various structural variations observed in TM helices of membrane proteins have been deconstructed into 9 distinct types of helix perturbations. These perturbations are defined by the deviation of TM helices from the predominantly observed linear α-helical conformation, to form 3 10 - and π-helices, as well as adopting curved and kinked geometries. The data presented here supplements the article 'Helix perturbations in Membrane Proteins Assist in Inter-helical Interactions and Optimal Helix Positioning in the Bilayer' (A. Shelar, M. Bansal, 2016) [1]. This data provides strong evidence for the role of various helix perturbations in influencing backbone torsion angles of helices, mediating inter-helical interactions, oligomer formation and accommodation of hydrophobic residues within the bilayer. The methodology used for creation of various datasets of membrane protein families (Sodium/Calcium exchanger and Heme Copper Oxidase) has also been mentioned.

Autoinhibition of ETV6 DNA Binding Is Established by the Stability of Its Inhibitory Helix

PubMed Central

De, Soumya; Okon, Mark; Graves, Barbara J.; McIntosh, Lawrence P.

2017-01-01

The ETS transcriptional repressor ETV6 (or TEL) is autoinhibited by an α-helix that sterically blocks its DNA-binding ETS domain. The inhibitory helix is marginally stable and unfolds when ETV6 binds to either specific or non-specific DNA. Using NMR spectroscopy, we show that folding of the inhibitory helix requires a buried charge–dipole interaction with helix H1 of the ETS domain. This interaction also contributes directly to autoinhibition by precluding a highly conserved dipole-enhanced hydrogen bond between the phosphodiester backbone of bound DNA and the N terminus of helix H1. To probe further the thermodynamic basis of autoinhibition, ETV6 variants were generated with amino acid substitutions introduced along the solvent exposed surface of the inhibitory helix. These changes were designed to increase the intrinsic helical propensity of the inhibitory helix without perturbing its packing interactions with the ETS domain. NMR-monitored amide hydrogen exchange measurements confirmed that the stability of the folded inhibitory helix increases progressively with added helix-promoting substitutions. This also results in progressively reinforced autoinhibition and decreased DNA-binding affinity. Surprisingly, locking the inhibitory helix onto the ETS domain by a disulfide bridge severely impairs, but does not abolish DNA binding. Weak interactions still occur via an interface displaced from the canonical ETS domain DNA-binding surface. Collectively, these studies establish a direct thermodynamic linkage between inhibitory helix stability and ETV6 autoinhibition, and demonstrate that helix unfolding does not strictly precede DNA binding. Modulating inhibitory helix stability provides a potential route for the in vivo regulation of ETV6 activity. PMID:26920109

Intramolecular triple helix as a model for regular polyribonucleotide (CAA)(n).

PubMed

Efimov, Alexander V; Spirin, Alexander S

2009-10-09

The regular (CAA)(n) polyribonucleotide, as well as the omega leader sequence containing (CAA)-rich core, have recently been shown to form cooperatively melted and compact structures. In this report, we propose a structural model for the (CAA)(n) sequence in which the polyribonucleotide chain is folded upon itself, so that it forms an intramolecular triple helix. The triple helix is stabilized by hydrogen bonding between bases thus forming coplanar triads, and by stacking interactions between the base triads. A distinctive feature of the proposed triple helix is that it does not contain the canonical double-helix elements. The difference from the known triple helices is that Watson-Crick hydrogen bond pairings do not take place in the interactions between the bases within the base triads.

Common fold in helix–hairpin–helix proteins

PubMed Central

Shao, Xuguang; Grishin, Nick V.

2000-01-01

Helix–hairpin–helix (HhH) is a widespread motif involved in non-sequence-specific DNA binding. The majority of HhH motifs function as DNA-binding modules, however, some of them are used to mediate protein–protein interactions or have acquired enzymatic activity by incorporating catalytic residues (DNA glycosylases). From sequence and structural analysis of HhH-containing proteins we conclude that most HhH motifs are integrated as a part of a five-helical domain, termed (HhH)2 domain here. It typically consists of two consecutive HhH motifs that are linked by a connector helix and displays pseudo-2-fold symmetry. (HhH)2 domains show clear structural integrity and a conserved hydrophobic core composed of seven residues, one residue from each α-helix and each hairpin, and deserves recognition as a distinct protein fold. In addition to known HhH in the structures of RuvA, RadA, MutY and DNA-polymerases, we have detected new HhH motifs in sterile alpha motif and barrier-to-autointegration factor domains, the α-subunit of Escherichia coli RNA-polymerase, DNA-helicase PcrA and DNA glyco­s­y­lases. Statistically significant sequence similarity of HhH motifs and pronounced structural conservation argue for homology between (HhH)2 domains in different protein families. Our analysis helps to clarify how non-symmetric protein motifs bind to the double helix of DNA through the formation of a pseudo-2-fold symmetric (HhH)2 functional unit. PMID:10908318

Theory of helix traveling wave tubes with dielectric and vane loading

DOE Office of Scientific and Technical Information (OSTI.GOV)

Freund, H.P.; Zaidman, E.G.; Antonsen, T.M. Jr.

1996-08-01

A time-dependent nonlinear analysis of a helix traveling wave tube (TWT) is presented for a configuration where an electron beam propagates through a sheath helix surrounded by a conducting wall. The effects of dielectric and vane loading are included in the formulation as is efficiency enhancement by tapering the helix pitch. Dielectric loading is described under the assumption that the gap between the helix and the wall is uniformly filled by a dielectric material. The vane-loading model describes the insertion of an arbitrary number of vanes running the length of the helix, and the polarization of the field between themore » vanes is assumed to be an azimuthally symmetric transverse-electric mode. The field is represented as a superposition of azimuthally symmetric waves in a vacuum sheath helix. An overall explicit sinusoidal variation of the form exp({ital ikz}{minus}{ital i}{omega}{ital t}) is assumed (where {omega} denotes the angular frequency corresponding to the wave number {ital k} in the vacuum sheath helix), and the polarization and radial variation of each wave is determined by the boundary conditions in a vacuum sheath helix. The propagation of each wave {ital in} {ital vacuo} as well as the interaction of each wave with the electron beam is included by allowing the amplitudes of the waves to vary in {ital z} and {ital t}. A dynamical equation for the field amplitudes is derived analogously to Poynting{close_quote}s equation, and solved in conjunction with the three-dimensional Lorentz force equations for an ensemble of electrons. Electron beams with a both a continuous and emission-gated pulse format are analyzed, and the model is compared with linear theory of the interaction as well as with the performance of a TWTs operated at the Naval Research Laboratory and at Northrop{endash}Grumman Corporation. {copyright} {ital 1996 American Institute of Physics.}« less

Iron-Binding E3 Ligase Mediates Iron Response in Plants by Targeting Basic Helix-Loop-Helix Transcription Factors1[OPEN

PubMed Central

Selote, Devarshi; Samira, Rozalynne; Matthiadis, Anna; Gillikin, Jeffrey W.; Long, Terri A.

2015-01-01

Iron uptake and metabolism are tightly regulated in both plants and animals. In Arabidopsis (Arabidopsis thaliana), BRUTUS (BTS), which contains three hemerythrin (HHE) domains and a Really Interesting New Gene (RING) domain, interacts with basic helix-loop-helix transcription factors that are capable of forming heterodimers with POPEYE (PYE), a positive regulator of the iron deficiency response. BTS has been shown to have E3 ligase capacity and to play a role in root growth, rhizosphere acidification, and iron reductase activity in response to iron deprivation. To further characterize the function of this protein, we examined the expression pattern of recombinant ProBTS::β-GLUCURONIDASE and found that it is expressed in developing embryos and other reproductive tissues, corresponding with its apparent role in reproductive growth and development. Our findings also indicate that the interactions between BTS and PYE-like (PYEL) basic helix-loop-helix transcription factors occur within the nucleus and are dependent on the presence of the RING domain. We provide evidence that BTS facilitates 26S proteasome-mediated degradation of PYEL proteins in the absence of iron. We also determined that, upon binding iron at the HHE domains, BTS is destabilized and that this destabilization relies on specific residues within the HHE domains. This study reveals an important and unique mechanism for plant iron homeostasis whereby an E3 ubiquitin ligase may posttranslationally control components of the transcriptional regulatory network involved in the iron deficiency response. PMID:25452667

Conformational dynamics of the inner pore helix of voltage-gated potassium channels

NASA Astrophysics Data System (ADS)

Choe, Seungho; Grabe, Michael

2009-06-01

Voltage-gated potassium (Kv) channels control the electrical excitability of neurons and muscles. Despite this key role, how these channels open and close or gate is not fully understood. Gating is usually attributed to the bending and straightening of pore-lining helices at glycine and proline residues. In this work we focused on the role of proline in the Pro-Val-Pro (PVP) motif of the inner S6 helix in the Kv1.2 channel. We started by developing a simple hinged-rod model to fully explore the configurational space of bent helices and we related these configurations to the degree of pore opening. We then carried out fully atomistic simulations of the S6 helices and compared these simulations to the hinged-rod model. Both methods suggest that Kv1 channels are not tightly closed when the inner helices are straight, unlike what is seen in the non-PVP containing channels KcsA and KirBac. These results invite the possibility that the S6 helices may be kinked when Kv1 channels are closed. Our simulations indicate that the wild-type helix adopts multiple spatially distinct configurations, which is consistent with its role in adopting a closed state and an open state. The two most dominant configurational basins correspond to a 6 Å movement of the helix tail accompanied by the PVP region undergoing a local α-helix to 310-helix transition. We explored how single point mutations affect the propensity of the S6 helix to adopt particular configurations. Interestingly, mutating the first proline, P405 (P473 in Shaker), to alanine completely removed the bistable nature of the S6 helix possibly explaining why this mutation compromises the channel. Next, we considered four other mutations in the area known to affect channel gating and we saw similarly dramatic changes to the helix's dynamics and range of motion. Our results suggest a possible mechanism of helix pore closure and they suggest differences in the closed state of glycine-only channels, like KcsA, and PVP containing

Direct folding simulation of a long helix in explicit water

NASA Astrophysics Data System (ADS)

Gao, Ya; Lu, Xiaoliang; Duan, Lili; Zhang, Dawei; Mei, Ye; Zhang, John Z. H.

2013-05-01

A recently proposed Polarizable Hydrogen Bond (PHB) method has been employed to simulate the folding of a 53 amino acid helix (PDB ID 2KHK) in explicit water. Under PHB simulation, starting from a fully extended structure, the peptide folds into the native state as confirmed by measured time evolutions of radius of gyration, root mean square deviation (RMSD), and native hydrogen bond. Free energy and cluster analysis show that the folded helix is thermally stable under the PHB model. Comparison of simulation results under, respectively, PHB and standard nonpolarizable force field demonstrates that polarization is critical for stable folding of this long α-helix.

IFSM fractal image compression with entropy and sparsity constraints: A sequential quadratic programming approach

NASA Astrophysics Data System (ADS)

Kunze, Herb; La Torre, Davide; Lin, Jianyi

2017-01-01

We consider the inverse problem associated with IFSM: Given a target function f , find an IFSM, such that its fixed point f ¯ is sufficiently close to f in the Lp distance. Forte and Vrscay [1] showed how to reduce this problem to a quadratic optimization model. In this paper, we extend the collage-based method developed by Kunze, La Torre and Vrscay ([2][3][4]), by proposing the minimization of the 1-norm instead of the 0-norm. In fact, optimization problems involving the 0-norm are combinatorial in nature, and hence in general NP-hard. To overcome these difficulties, we introduce the 1-norm and propose a Sequential Quadratic Programming algorithm to solve the corresponding inverse problem. As in Kunze, La Torre and Vrscay [3] in our formulation, the minimization of collage error is treated as a multi-criteria problem that includes three different and conflicting criteria i.e., collage error, entropy and sparsity. This multi-criteria program is solved by means of a scalarization technique which reduces the model to a single-criterion program by combining all objective functions with different trade-off weights. The results of some numerical computations are presented.

Origin and Diversification of Basic-Helix-Loop-Helix Proteins in Plants

PubMed Central

Pires, Nuno; Dolan, Liam

2010-01-01

Basic helix-loop-helix (bHLH) proteins are a class of transcription factors found throughout eukaryotic organisms. Classification of the complete sets of bHLH proteins in the sequenced genomes of Arabidopsis thaliana and Oryza sativa (rice) has defined the diversity of these proteins among flowering plants. However, the evolutionary relationships of different plant bHLH groups and the diversity of bHLH proteins in more ancestral groups of plants are currently unknown. In this study, we use whole-genome sequences from nine species of land plants and algae to define the relationships between these proteins in plants. We show that few (less than 5) bHLH proteins are encoded in the genomes of chlorophytes and red algae. In contrast, many bHLH proteins (100–170) are encoded in the genomes of land plants (embryophytes). Phylogenetic analyses suggest that plant bHLH proteins are monophyletic and constitute 26 subfamilies. Twenty of these subfamilies existed in the common ancestors of extant mosses and vascular plants, whereas six further subfamilies evolved among the vascular plants. In addition to the conserved bHLH domains, most subfamilies are characterized by the presence of highly conserved short amino acid motifs. We conclude that much of the diversity of plant bHLH proteins was established in early land plants, over 440 million years ago. PMID:19942615

Regional Dimensions of the Triple Helix Model: Setting the Context

ERIC Educational Resources Information Center

Todeva, Emanuela; Danson, Mike

2016-01-01

This paper introduces the rationale for the special issue and its contributions, which bridge the literature on regional development and the Triple Helix model. The concept of the Triple Helix at the sub-national, and specifically regional, level is established and examined, with special regard to regional economic development founded on…

Reflections on the ambivalent helix.

PubMed

Galloway, J W

1989-09-15

The helix is nature's favourite shape. Because of its elementary geometry and distinctive appearance it is also the clearest instance of an enantiomorphic object--a helix and its mirror image are identical in all respects except their screw sense. This is a distinction that can be ignored from the points of view of pure geometry and pure group theory but any helical structure is actually available as either or both hands. Whether in nature helices do occur as just one hand, or both, is one of the best--perhaps the best--puzzles of the science of form. In this short review I look at a few examples of naturally occurring helices, some where only one hand is found, some where both are commonly found, and perhaps the most interesting examples in biological terms--those where both are found but one hand is very much rarer than the other. I review what mechanisms--physico-chemical, genetic, evolutionary--underlie the different manifestations of left- and right-handedness.

WRF-TMH: predicting transmembrane helix by fusing composition index and physicochemical properties of amino acids.

PubMed

Hayat, Maqsood; Khan, Asifullah

2013-05-01

Membrane protein is the prime constituent of a cell, which performs a role of mediator between intra and extracellular processes. The prediction of transmembrane (TM) helix and its topology provides essential information regarding the function and structure of membrane proteins. However, prediction of TM helix and its topology is a challenging issue in bioinformatics and computational biology due to experimental complexities and lack of its established structures. Therefore, the location and orientation of TM helix segments are predicted from topogenic sequences. In this regard, we propose WRF-TMH model for effectively predicting TM helix segments. In this model, information is extracted from membrane protein sequences using compositional index and physicochemical properties. The redundant and irrelevant features are eliminated through singular value decomposition. The selected features provided by these feature extraction strategies are then fused to develop a hybrid model. Weighted random forest is adopted as a classification approach. We have used two benchmark datasets including low and high-resolution datasets. tenfold cross validation is employed to assess the performance of WRF-TMH model at different levels including per protein, per segment, and per residue. The success rates of WRF-TMH model are quite promising and are the best reported so far on the same datasets. It is observed that WRF-TMH model might play a substantial role, and will provide essential information for further structural and functional studies on membrane proteins. The accompanied web predictor is accessible at http://111.68.99.218/WRF-TMH/ .

Elevated temperature triggers human respiratory syncytial virus F protein six-helix bundle formation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yunus, Abdul S.; Jackson, Trent P.; Crisafi, Katherine

2010-01-20

Human respiratory syncytial virus (RSV) is a major cause of severe lower respiratory tract infection in infants, immunocompromised patients, and the elderly. The RSV fusion (F) protein mediates fusion of the viral envelope with the target cell membrane during virus entry and is a primary target for antiviral drug and vaccine development. The F protein contains two heptad repeat regions, HR1 and HR2. Peptides corresponding to these regions form a six-helix bundle structure that is thought to play a critical role in membrane fusion. However, characterization of six-helix bundle formation in native RSV F protein has been hindered by themore » fact that a trigger for F protein conformational change has yet to be identified. Here we demonstrate that RSV F protein on the surface of infected cells undergoes a conformational change following exposure to elevated temperature, resulting in the formation of the six-helix bundle structure. We first generated and characterized six-helix bundle-specific antibodies raised against recombinant peptides modeling the RSV F protein six-helix bundle structure. We then used these antibodies as probes to monitor RSV F protein six-helix bundle formation in response to a diverse array of potential triggers of conformational changes. We found that exposure of 'membrane-anchored' RSV F protein to elevated temperature (45-55 deg. C) was sufficient to trigger six-helix bundle formation. Antibody binding to the six-helix bundle conformation was detected by both flow cytometry and cell-surface immunoprecipitation of the RSV F protein. None of the other treatments, including interaction with a number of potential receptors, resulted in significant binding by six-helix bundle-specific antibodies. We conclude that native, untriggered RSV F protein exists in a metastable state that can be converted in vitro to the more stable, fusogenic six-helix bundle conformation by an increase in thermal energy. These findings help to better define the

The CDRH Helix: an in vivo evaluation.

PubMed

Anhalt, D; Hynynen, K; DeYoung, D; Shimm, D; Kundrat, M; Cetas, T

1990-01-01

The Helix is an electromagnetic heating device used to induce regional/systemic hyperthermia for cancer therapy. It is a resonant device operating at about 82 MHz with an aperture size of 60 cm x 40 cm (elliptical) x 40 cm long. The Helix deposits power in tissues (or phantoms) by producing a predominantly axial electric field within its radiating aperture. Five pig experiments were performed to provide in vivo verification of specific absorption rate (SAR) measurements and electric field measurements which were obtained earlier in tissue-equivalent phantom and 0.9% saline, respectively. In addition to verifying the power deposition patterns found in phantoms, the pig experiments provided valuable insight into the capabilities and limitations of electromagnetic regional heating. For example, a kidney with limited blood flow, simulating a necrotic tumor, heated very well-although the highest temperature was not always measured there. Also, fat heating may be a problem, since excessive temperatures in the fat were observed in approximately 20% of the heatings. This paper compares the in vivo temperature measurements in pigs with SARs and electric field measurements obtained in phantoms, and also provides a brief overview of results of the Helix in clinical situations.

Probing the Non-Native H Helix Translocation in Apomyoglobin Folding Intermediates

PubMed Central

2015-01-01

Apomyoglobin folds via sequential helical intermediates that are formed by rapid collapse of the A, B, G, and H helix regions. An equilibrium molten globule with a similar structure is formed near pH 4. Previous studies suggested that the folding intermediates are kinetically trapped states in which folding is impeded by non-native packing of the G and H helices. Fluorescence spectra of mutant proteins in which cysteine residues were introduced at several positions in the G and H helices show differential quenching of W14 fluorescence, providing direct evidence of translocation of the H helix relative to helices A and G in both the kinetic and equilibrium intermediates. Förster resonance energy transfer measurements show that a 5-({2-[(acetyl)amino]ethyl}amino)naphthalene-1-sulfonic acid acceptor coupled to K140C (helix H) is closer to Trp14 (helix A) in the equilibrium molten globule than in the native state, by a distance that is consistent with sliding of the H helix in an N-terminal direction by approximately one helical turn. Formation of an S108C–L135C disulfide prevents H helix translocation in the equilibrium molten globule by locking the G and H helices into their native register. By enforcing nativelike packing of the A, G, and H helices, the disulfide resolves local energetic frustration and facilitates transient docking of the E helix region onto the hydrophobic core but has only a small effect on the refolding rate. The apomyoglobin folding landscape is highly rugged, with several energetic bottlenecks that frustrate folding; relief of any one of the major identified bottlenecks is insufficient to speed progression to the transition state. PMID:24857522

Crosslinked Aspartic Acids as Helix-Nucleating Templates.

PubMed

Zhao, Hui; Liu, Qi-Song; Geng, Hao; Tian, Yuan; Cheng, Min; Jiang, Yan-Hong; Xie, Ming-Sheng; Niu, Xiao-Gang; Jiang, Fan; Zhang, Ya-Ou; Lao, Yuan-Zhi; Wu, Yun-Dong; Xu, Nai-Han; Li, Zi-Gang

2016-09-19

Described is a facile helix-nucleating template based on a tethered aspartic acid at the N-terminus [terminal aspartic acid (TD)]. The nucleating effect of the template is subtly influenced by the substituent at the end of the side-chain-end tether as indicated by circular dichroism, nuclear magnetic resonance, and molecular dynamics simulations. Unlike most nucleating strategies, the N-terminal amine is preserved, thus enabling further modification. Peptidomimetic estrogen receptor modulators (PERMs) constructed using this strategy show improved therapeutic properties. The current strategy can be regarded as a good complement to existing helix-stabilizing methods. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Helix-length compensation studies reveal the adaptability of the VS ribozyme architecture.

PubMed

Lacroix-Labonté, Julie; Girard, Nicolas; Lemieux, Sébastien; Legault, Pascale

2012-03-01

Compensatory mutations in RNA are generally regarded as those that maintain base pairing, and their identification forms the basis of phylogenetic predictions of RNA secondary structure. However, other types of compensatory mutations can provide higher-order structural and evolutionary information. Here, we present a helix-length compensation study for investigating structure-function relationships in RNA. The approach is demonstrated for stem-loop I and stem-loop V of the Neurospora VS ribozyme, which form a kissing-loop interaction important for substrate recognition. To rapidly characterize the substrate specificity (k(cat)/K(M)) of several substrate/ribozyme pairs, a procedure was established for simultaneous kinetic characterization of multiple substrates. Several active substrate/ribozyme pairs were identified, indicating the presence of limited substrate promiscuity for stem Ib variants and helix-length compensation between stems Ib and V. 3D models of the I/V interaction were generated that are compatible with the kinetic data. These models further illustrate the adaptability of the VS ribozyme architecture for substrate cleavage and provide global structural information on the I/V kissing-loop interaction. By exploring higher-order compensatory mutations in RNA our approach brings a deeper understanding of the adaptability of RNA structure, while opening new avenues for RNA research.

Thymocyte Maturation Is Regulated by the Activity of the Helix-Loop-Helix Protein, E47

PubMed Central

Bain, Gretchen; Quong, Melanie W.; Soloff, Rachel S.; Hedrick, Stephen M.; Murre, Cornelis

1999-01-01

The E2A proteins, E12 and E47, are required for progression through multiple developmental pathways, including early B and T lymphopoiesis. Here, we provide in vitro and in vivo evidence demonstrating that E47 activity regulates double-positive thymocyte maturation. In the absence of E47 activity, positive selection of both major histocompatibility complex (MHC) class I– and class II–restricted T cell receptors (TCRs) is perturbed. Additionally, development of CD8 lineage T cells in an MHC class I–restricted TCR transgenic background is sensitive to the dosage of E47. Mice deficient for E47 display an increase in production of mature CD4 and CD8 lineage T cells. Furthermore, ectopic expression of an E2A inhibitor helix-loop-helix protein, Id3, promotes the in vitro differentiation of an immature T cell line. These results demonstrate that E2A functions as a regulator of thymocyte positive selection. PMID:10587351

HELIX: The High Energy Light Isotope Experiment

NASA Astrophysics Data System (ADS)

Wakely, Scott

This is the lead proposal for a new suborbital program, HELIX (High-Energy Light Isotope eXperiment), designed to make measurements of the isotopic composition of light cosmic-ray nuclei from ~200 MeV/nuc to ~10 GeV/nuc. Past measurements of this kind have provided profound insights into the nature and origin of cosmic rays, revealing, for instance, information on acceleration and confinement time scales, and exposing some conspicuous discrepancies between solar and cosmic-ray abundances. The most detailed information currently available comes from the ACE/CRIS mission, but is restricted to energies below a few 100 MeV/nuc. HELIX aims at extending this energy range by over an order of magnitude, where, in most cases, no measurements of any kind exist, and where relativistic time dilation affects the apparent lifetime of radioactive clock nuclei. The HELIX measurements will provide essential information for understanding the propagation history of cosmic rays in the galaxy. This is crucial for properly interpreting several intriguing anomalies reported in recent cosmic-ray measurements, pertaining to the energy spectra of protons, helium, and heavier nuclei, and to the anomalous rise in the positron fraction at higher energy. HELIX employs a high-precision magnet spectrometer to provide measurements which are not achievable by any current or planned instrument. The superconducting magnet originally used for the HEAT payload in five successful high-altitude flights will be combined with state-of-the-art detectors to measure the charge, time-of-flight, magnetic rigidity, and velocity of cosmic-ray particles with high precision. The instrumentation includes plastic scintillators, silicon-strip detectors repurposed from Fermilab's CDF detector, a high-performance gas drift chamber, and a ring-imaging Cherenkov counter employing aerogel radiators and silicon photomultipliers. To reduce cost and technical risk, the HELIX program will be structured in two stages. The first

Genome-wide identification and analysis of the chicken basic helix-loop-helix factors.

PubMed

Liu, Wu-Yi; Zhao, Chun-Jiang

2010-01-01

Members of the basic helix-loop-helix (bHLH) family of transcription factors play important roles in a wide range of developmental processes. In this study, we conducted a genome-wide survey using the chicken (Gallus gallus) genomic database, and identified 104 bHLH sequences belonging to 42 gene families in an effort to characterize the chicken bHLH transcription factor family. Phylogenetic analyses revealed that chicken has 50, 21, 15, 4, 8, and 3 bHLH members in groups A, B, C, D, E, and F, respectively, while three members belonging to none of these groups were classified as ''orphans". A comparison between chicken and human bHLH repertoires suggested that both organisms have a number of lineage-specific bHLH members in the proteomes. Chromosome distribution patterns and phylogenetic analyses strongly suggest that the bHLH members should have arisen through gene duplication at an early date. Gene Ontology (GO) enrichment statistics showed 51 top GO annotations of biological processes counted in the frequency. The present study deepens our understanding of the chicken bHLH transcription factor family and provides much useful information for further studies using chicken as a model system.

Elastic Model Transitions: a Hybrid Approach Utilizing Quadratic Inequality Constrained Least Squares (LSQI) and Direct Shape Mapping (DSM)

NASA Technical Reports Server (NTRS)

Jurenko, Robert J.; Bush, T. Jason; Ottander, John A.

2014-01-01

A method for transitioning linear time invariant (LTI) models in time varying simulation is proposed that utilizes both quadratically constrained least squares (LSQI) and Direct Shape Mapping (DSM) algorithms to determine physical displacements. This approach is applicable to the simulation of the elastic behavior of launch vehicles and other structures that utilize multiple LTI finite element model (FEM) derived mode sets that are propagated throughout time. The time invariant nature of the elastic data for discrete segments of the launch vehicle trajectory presents a problem of how to properly transition between models while preserving motion across the transition. In addition, energy may vary between flex models when using a truncated mode set. The LSQI-DSM algorithm can accommodate significant changes in energy between FEM models and carries elastic motion across FEM model transitions. Compared with previous approaches, the LSQI-DSM algorithm shows improvements ranging from a significant reduction to a complete removal of transients across FEM model transitions as well as maintaining elastic motion from the prior state.

A genome-wide survey on basic helix-loop-helix transcription factors in giant panda.

PubMed

Dang, Chunwang; Wang, Yong; Zhang, Debao; Yao, Qin; Chen, Keping

2011-01-01

The giant panda (Ailuropoda melanoleuca) is a critically endangered mammalian species. Studies on functions of regulatory proteins involved in developmental processes would facilitate understanding of specific behavior in giant panda. The basic helix-loop-helix (bHLH) proteins play essential roles in a wide range of developmental processes in higher organisms. bHLH family members have been identified in over 20 organisms, including fruit fly, zebrafish, mouse and human. Our present study identified 107 bHLH family members being encoded in giant panda genome. Phylogenetic analyses revealed that they belong to 44 bHLH families with 46, 25, 15, 4, 11 and 3 members in group A, B, C, D, E and F, respectively, while the remaining 3 members were assigned into "orphan". Compared to mouse, the giant panda does not encode seven bHLH proteins namely Beta3a, Mesp2, Sclerax, S-Myc, Hes5 (or Hes6), EBF4 and Orphan 1. These results provide useful background information for future studies on structure and function of bHLH proteins in the regulation of giant panda development.

Transmembrane helix prediction: a comparative evaluation and analysis.

PubMed

Cuthbertson, Jonathan M; Doyle, Declan A; Sansom, Mark S P

2005-06-01

The prediction of transmembrane (TM) helices plays an important role in the study of membrane proteins, given the relatively small number (approximately 0.5% of the PDB) of high-resolution structures for such proteins. We used two datasets (one redundant and one non-redundant) of high-resolution structures of membrane proteins to evaluate and analyse TM helix prediction. The redundant (non-redundant) dataset contains structure of 434 (268) TM helices, from 112 (73) polypeptide chains. Of the 434 helices in the dataset, 20 may be classified as 'half-TM' as they are too short to span a lipid bilayer. We compared 13 TM helix prediction methods, evaluating each method using per segment, per residue and termini scores. Four methods consistently performed well: SPLIT4, TMHMM2, HMMTOP2 and TMAP. However, even the best methods were in error by, on average, about two turns of helix at the TM helix termini. The best and worst case predictions for individual proteins were analysed. In particular, the performance of the various methods and of a consensus prediction method, were compared for a number of proteins (e.g. SecY, ClC, KvAP) containing half-TM helices. The difficulties of predicting half-TM helices suggests that current prediction methods successfully embody the two-state model of membrane protein folding, but do not accommodate a third stage in which, e.g., short helices and re-entrant loops fold within a bundle of stable TM helices.

Organizing product innovation: hierarchy, market or triple-helix networks?

PubMed

Fitjar, Rune Dahl; Gjelsvik, Martin; Rodríguez-Pose, Andrés

This paper assesses the extent to which the organization of the innovation effort in firms, as well as the geographical scale at which this effort is pursued, affects the capacity to benefit from product innovations. Three alternative modes of organization are studied: hierarchy, market and triple-helix-type networks. Furthermore, we consider triple-helix networks at three geographical scales: local, national and international. These relationships are tested on a random sample of 763 firms located in five urban regions of Norway which reported having introduced new products or services during the preceding 3 years. The analysis shows that firms exploiting internal hierarchy or triple-helix networks with a wide range of partners managed to derive a significantly higher share of their income from new products, compared to those that mainly relied on outsourcing within the market. In addition, the analysis shows that the geographical scale of cooperation in networks, as well as the type of partner used, matters for the capacity of firms to benefit from product innovation. In particular, firms that collaborate in international triple-helix-type networks involving suppliers, customers and R&D institutions extract a higher share of their income from product innovations, regardless of whether they organize the processes internally or through the network.

The signaling helix: a common functional theme in diverse signaling proteins

PubMed Central

Anantharaman, Vivek; Balaji, S; Aravind, L

2006-01-01

Background The mechanism by which the signals are transmitted between receptor and effector domains in multi-domain signaling proteins is poorly understood. Results Using sensitive sequence analysis methods we identify a conserved helical segment of around 40 residues in a wide range of signaling proteins, including numerous sensor histidine kinases such as Sln1p, and receptor guanylyl cyclases such as the atrial natriuretic peptide receptor and nitric oxide receptors. We term this helical segment the signaling (S)-helix and present evidence that it forms a novel parallel coiled-coil element, distinct from previously known helical segments in signaling proteins, such as the Dimerization-Histidine phosphotransfer module of histidine kinases, the intra-cellular domains of the chemotaxis receptors, inter-GAF domain helical linkers and the α-helical HAMP module. Analysis of domain architectures allowed us to reconstruct the domain-neighborhood graph for the S-helix, which showed that the S-helix almost always occurs between two signaling domains. Several striking patterns in the domain neighborhood of the S-helix also became evident from the graph. It most often separates diverse N-terminal sensory domains from various C-terminal catalytic signaling domains such as histidine kinases, cNMP cyclase, PP2C phosphatases, NtrC-like AAA+ ATPases and diguanylate cyclases. It might also occur between two sensory domains such as PAS domains and occasionally between a DNA-binding HTH domain and a sensory domain. The sequence conservation pattern of the S-helix revealed the presence of a unique constellation of polar residues in the dimer-interface positions within the central heptad of the coiled-coil formed by the S-helix. Conclusion Combining these observations with previously reported mutagenesis studies on different S-helix-containing proteins we suggest that it functions as a switch that prevents constitutive activation of linked downstream signaling domains. However, upon

An efficient inverse radiotherapy planning method for VMAT using quadratic programming optimization.

PubMed

Hoegele, W; Loeschel, R; Merkle, N; Zygmanski, P

2012-01-01

The purpose of this study is to investigate the feasibility of an inverse planning optimization approach for the Volumetric Modulated Arc Therapy (VMAT) based on quadratic programming and the projection method. The performance of this method is evaluated against a reference commercial planning system (eclipse(TM) for rapidarc(TM)) for clinically relevant cases. The inverse problem is posed in terms of a linear combination of basis functions representing arclet dose contributions and their respective linear coefficients as degrees of freedom. MLC motion is decomposed into basic motion patterns in an intuitive manner leading to a system of equations with a relatively small number of equations and unknowns. These equations are solved using quadratic programming under certain limiting physical conditions for the solution, such as the avoidance of negative dose during optimization and Monitor Unit reduction. The modeling by the projection method assures a unique treatment plan with beneficial properties, such as the explicit relation between organ weightings and the final dose distribution. Clinical cases studied include prostate and spine treatments. The optimized plans are evaluated by comparing isodose lines, DVH profiles for target and normal organs, and Monitor Units to those obtained by the clinical treatment planning system eclipse(TM). The resulting dose distributions for a prostate (with rectum and bladder as organs at risk), and for a spine case (with kidneys, liver, lung and heart as organs at risk) are presented. Overall, the results indicate that similar plan qualities for quadratic programming (QP) and rapidarc(TM) could be achieved at significantly more efficient computational and planning effort using QP. Additionally, results for the quasimodo phantom [Bohsung et al., "IMRT treatment planning: A comparative inter-system and inter-centre planning exercise of the estro quasimodo group," Radiother. Oncol. 76(3), 354-361 (2005)] are presented as an example

A class of stochastic optimization problems with one quadratic & several linear objective functions and extended portfolio selection model

NASA Astrophysics Data System (ADS)

Xu, Jiuping; Li, Jun

2002-09-01

In this paper a class of stochastic multiple-objective programming problems with one quadratic, several linear objective functions and linear constraints has been introduced. The former model is transformed into a deterministic multiple-objective nonlinear programming model by means of the introduction of random variables' expectation. The reference direction approach is used to deal with linear objectives and results in a linear parametric optimization formula with a single linear objective function. This objective function is combined with the quadratic function using the weighted sums. The quadratic problem is transformed into a linear (parametric) complementary problem, the basic formula for the proposed approach. The sufficient and necessary conditions for (properly, weakly) efficient solutions and some construction characteristics of (weakly) efficient solution sets are obtained. An interactive algorithm is proposed based on reference direction and weighted sums. Varying the parameter vector on the right-hand side of the model, the DM can freely search the efficient frontier with the model. An extended portfolio selection model is formed when liquidity is considered as another objective to be optimized besides expectation and risk. The interactive approach is illustrated with a practical example.

VIEW OF EAST ELEVATION OF HELIX HOUSE NO. 2 (S87), ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

VIEW OF EAST ELEVATION OF HELIX HOUSE NO. 2 (S-87), LOOKING WEST (without scale stick). - Naval Computer & Telecommunications Area Master Station, Eastern Pacific, Radio Transmitter Facility Lualualei, Helix House No. 2, Base of Radio Antenna Structure No. 427, Makaha, Honolulu County, HI

VIEW OF EAST ELEVATION OF HELIX HOUSE NO. 2 (S87), ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

VIEW OF EAST ELEVATION OF HELIX HOUSE NO. 2 (S-87), LOOKING WEST (with scale stick). - Naval Computer & Telecommunications Area Master Station, Eastern Pacific, Radio Transmitter Facility Lualualei, Helix House No. 2, Base of Radio Antenna Structure No. 427, Makaha, Honolulu County, HI

Quadratic formula for determining the drop size in pressure-atomized sprays with and without swirl

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, T.-W, E-mail: attwl@asu.edu; An, Keju

2016-06-15

We use a theoretical framework based on the integral form of the conservation equations, along with a heuristic model of the viscous dissipation, to find a closed-form solution to the liquid atomization problem. The energy balance for the spray renders to a quadratic formula for the drop size as a function, primarily of the liquid velocity. The Sauter mean diameter found using the quadratic formula shows good agreements and physical trends, when compared with experimental observations. This approach is shown to be applicable toward specifying initial drop size in computational fluid dynamics of spray flows.

An application of nonlinear programming to the design of regulators of a linear-quadratic formulation

NASA Technical Reports Server (NTRS)

Fleming, P.

1983-01-01

A design technique is proposed for linear regulators in which a feedback controller of fixed structure is chosen to minimize an integral quadratic objective function subject to the satisfaction of integral quadratic constraint functions. Application of a nonlinear programming algorithm to this mathematically tractable formulation results in an efficient and useful computer aided design tool. Particular attention is paid to computational efficiency and various recommendations are made. Two design examples illustrate the flexibility of the approach and highlight the special insight afforded to the designer. One concerns helicopter longitudinal dynamics and the other the flight dynamics of an aerodynamically unstable aircraft.

The stability of quadratic-reciprocal functional equation

NASA Astrophysics Data System (ADS)

Song, Aimin; Song, Minwei

2018-04-01

A new quadratic-reciprocal functional equation f ((k +1 )x +k y )+f ((k +1 )x -k y )=2/f (x )f (y )[(k+1 ) 2f (y )+k2f (x )] [(k+1)2f (y )-k2f (x )] 2 is introduced. The Hyers-Ulam stability for the quadratic-reciprocal functional equations is proved in Banach spaces using the direct method and the fixed point method, respectively.

Test spaces and characterizations of quadratic spaces

NASA Astrophysics Data System (ADS)

Dvurečenskij, Anatolij

1996-10-01

We show that a test space consisting of nonzero vectors of a quadratic space E and of the set all maximal orthogonal systems in E is algebraic iff E is Dacey or, equivalently, iff E is orthomodular. In addition, we present another orthomodularity criteria of quadratic spaces, and using the result of Solèr, we show that they can imply that E is a real, complex, or quaternionic Hilbert space.

Geometric quadratic stochastic operator on countable infinite set

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ganikhodjaev, Nasir; Hamzah, Nur Zatul Akmar

2015-02-03

In this paper we construct the family of Geometric quadratic stochastic operators defined on the countable sample space of nonnegative integers and investigate their trajectory behavior. Such operators can be reinterpreted in terms of of evolutionary operator of free population. We show that Geometric quadratic stochastic operators are regular transformations.

A Secondary Structural Transition in the C-helix Promotes Gating of Cyclic Nucleotide-regulated Ion Channels*

PubMed Central

Puljung, Michael C.; Zagotta, William N.

2013-01-01

Cyclic nucleotide-regulated ion channels bind second messengers like cAMP to a C-terminal domain, consisting of a β-roll, followed by two α-helices (B- and C-helices). We monitored the cAMP-dependent changes in the structure of the C-helix of a C-terminal fragment of HCN2 channels using transition metal ion FRET between fluorophores on the C-helix and metal ions bound between histidine pairs on the same helix. cAMP induced a change in the dimensions of the C-helix and an increase in the metal binding affinity of the histidine pair. cAMP also caused an increase in the distance between a fluorophore on the C-helix and metal ions bound to the B-helix. Stabilizing the C-helix of intact CNGA1 channels by metal binding to a pair of histidines promoted channel opening. These data suggest that ordering of the C-helix is part of the gating conformational change in cyclic nucleotide-regulated channels. PMID:23525108

Empirical parameterization of a model for predicting peptide helix/coil equilibrium populations.

PubMed Central

Andersen, N. H.; Tong, H.

1997-01-01

A modification of the Lifson-Roig formulation of helix/coil transitions is presented; it (1) incorporates end-capping and coulombic (salt bridges, hydrogen bonding, and side-chain interactions with charged termini and the helix dipole) effects, (2) helix-stabilizing hydrophobic clustering, (3) allows for different inherent termination probabilities of individual residues, and (4) differentiates helix elongation in the first versus subsequent turns of a helix. Each residue is characterized by six parameters governing helix formation. The formulation of the conditional probability of helix initiation and termination that we developed is essentially the same as one presented previously (Shalongo W, Stellwagen, E. 1995. Protein Sci 4:1161-1166) and nearly the mathematical equivalent of the new capping formulation incorporated in the model presented by Rohl et al. (1996. Protein Sci 5:2623-2637). Side-chain/side-chain interactions are, in most cases, incorporated as context dependent modifications of propagation rather than nucleation parameters. An alternative procedure for converting [theta]221 values to experimental fractional helicities () is presented. Tests of the program predictions suggest this method may have some advantages both for designed peptides and for the analysis of secondary structure preferences that could drive the formation of molten-globule intermediates on protein folding pathways. The model predicts the fractional helicity of 385 peptides with a root-mean-square deviation (RMSD) of 0.050 and locates (with precise definition of the termini in many cases) helices in proteins as well as competing methods. The propagation and nucleation parameters were derived from NMR data and from the CD data for a 79 peptide "learning set" for which an excellent fit resulted (RMSD = 0.0295). The current set of parameter corrections for capping boxes, helix dipole interactions, and side-chain/side-chain interactions (coulombic, hydrogen bonding and hydrophobic

Transmembrane Polyproline Helix.

PubMed

Kubyshkin, Vladimir; Grage, Stephan L; Bürck, Jochen; Ulrich, Anne S; Budisa, Nediljko

2018-05-03

The third most abundant polypeptide conformation in nature, the polyproline-II helix, is a polar, extended secondary structure with a local organization stabilized by intercarbonyl interactions within the peptide chain. Here we design a hydrophobic polyproline-II helical peptide based on an oligomeric octahydroindole-2-carboxylic acid scaffold and demonstrate its transmembrane alignment in model lipid bilayers by means of solid-state 19 F NMR. As result, we provide a first example of a purely artificial transmembrane peptide with a structural organization that is not based on hydrogen-bonding.

VIEW OF SOUTH ELEVATION OF HELIX HOUSE NO. 2 (S87) ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

VIEW OF SOUTH ELEVATION OF HELIX HOUSE NO. 2 (S-87) SHOWING MAIN ENTRY DOOR, LOOKING NORTH NORTHWEST. - Naval Computer & Telecommunications Area Master Station, Eastern Pacific, Radio Transmitter Facility Lualualei, Helix House No. 2, Base of Radio Antenna Structure No. 427, Makaha, Honolulu County, HI

VIEW OF HELIX HOUSE NO. 2 (S87), WITH ANTENNA TOWER ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

VIEW OF HELIX HOUSE NO. 2 (S-87), WITH ANTENNA TOWER CABLE SUPPORT IN FOREGROUND, LOOKING SOUTHEAST. - Naval Computer & Telecommunications Area Master Station, Eastern Pacific, Radio Transmitter Facility Lualualei, Helix House No. 2, Base of Radio Antenna Structure No. 427, Makaha, Honolulu County, HI

Wind turbine power tracking using an improved multimodel quadratic approach.

PubMed

Khezami, Nadhira; Benhadj Braiek, Naceur; Guillaud, Xavier

2010-07-01

In this paper, an improved multimodel optimal quadratic control structure for variable speed, pitch regulated wind turbines (operating at high wind speeds) is proposed in order to integrate high levels of wind power to actively provide a primary reserve for frequency control. On the basis of the nonlinear model of the studied plant, and taking into account the wind speed fluctuations, and the electrical power variation, a multimodel linear description is derived for the wind turbine, and is used for the synthesis of an optimal control law involving a state feedback, an integral action and an output reference model. This new control structure allows a rapid transition of the wind turbine generated power between different desired set values. This electrical power tracking is ensured with a high-performance behavior for all other state variables: turbine and generator rotational speeds and mechanical shaft torque; and smooth and adequate evolution of the control variables. 2010 ISA. Published by Elsevier Ltd. All rights reserved.

Quadratic Programming for Allocating Control Effort

NASA Technical Reports Server (NTRS)

Singh, Gurkirpal

2005-01-01

A computer program calculates an optimal allocation of control effort in a system that includes redundant control actuators. The program implements an iterative (but otherwise single-stage) algorithm of the quadratic-programming type. In general, in the quadratic-programming problem, one seeks the values of a set of variables that minimize a quadratic cost function, subject to a set of linear equality and inequality constraints. In this program, the cost function combines control effort (typically quantified in terms of energy or fuel consumed) and control residuals (differences between commanded and sensed values of variables to be controlled). In comparison with prior control-allocation software, this program offers approximately equal accuracy but much greater computational efficiency. In addition, this program offers flexibility, robustness to actuation failures, and a capability for selective enforcement of control requirements. The computational efficiency of this program makes it suitable for such complex, real-time applications as controlling redundant aircraft actuators or redundant spacecraft thrusters. The program is written in the C language for execution in a UNIX operating system.

Compressive response and helix formation of a semiflexible polymer confined in a nanochannel

NASA Astrophysics Data System (ADS)

Hayase, Yumino; Sakaue, Takahiro; Nakanishi, Hiizu

2017-05-01

Configurations of a single semiflexible polymer is studied when it is pushed into a nanochannel in the case where the polymer persistence length lp is much longer than the channel diameter D :lp/D ≫1 . Using numerical simulations, we show that the polymer undergoes a sequence of recurring structural transitions upon longitudinal compression: random deflection along the channel, a helix going around the channel wall, double-fold random deflection, double-fold helix, etc. We find that the helix transition can be understood as buckling of deflection segments, and the initial helix formation takes place at very small compression with no appreciable weak compression regime of the random deflection polymer.

Some Paradoxical Results for the Quadratically Weighted Kappa

ERIC Educational Resources Information Center

Warrens, Matthijs J.

2012-01-01

The quadratically weighted kappa is the most commonly used weighted kappa statistic for summarizing interrater agreement on an ordinal scale. The paper presents several properties of the quadratically weighted kappa that are paradoxical. For agreement tables with an odd number of categories "n" it is shown that if one of the raters uses the same…

Health and Environment Linked for Information Exchange (HELIX)-Atlanta: A CDC-NASA Joint Environmental Public Health Tracking Collaborative Project

NASA Technical Reports Server (NTRS)

Al-Hamdan, Mohammad; Luvall, Jeff; Crosson, Bill; Estes, Maury; Limaye, Ashutosh; Quattrochi, Dale; Rickman, Doug

2008-01-01

HELIX-Atlanta was developed to support current and future state and local EPHT programs to implement data linking demonstration projects which could be part of the CDC EPHT Network. HELIX-Atlanta is a pilot linking project in Atlanta for CDC to learn about the challenges the states will encounter. NASA/MSFC and the CDC are partners in linking environmental and health data to enhance public health surveillance. The use of NASA technology creates value added geospatial products from existing environmental data sources to facilitate public health linkages. Proving the feasibility of the approach is the main objective

Hidden supersymmetry and quadratic deformations of the space-time conformal superalgebra

NASA Astrophysics Data System (ADS)

Yates, L. A.; Jarvis, P. D.

2018-04-01

We analyze the structure of the family of quadratic superalgebras, introduced in Jarvis et al (2011 J. Phys. A: Math. Theor. 44 235205), for the quadratic deformations of N  =  1 space-time conformal supersymmetry. We characterize in particular the ‘zero-step’ modules for this case. In such modules, the odd generators vanish identically, and the quadratic superalgebra is realized on a single irreducible representation of the even subalgebra (which is a Lie algebra). In the case under study, the quadratic deformations of N  =  1 space-time conformal supersymmetry, it is shown that each massless positive energy unitary irreducible representation (in the standard classification of Mack), forms such a zero-step module, for an appropriate parameter choice amongst the quadratic family (with vanishing central charge). For these massless particle multiplets therefore, quadratic supersymmetry is unbroken, in that the supersymmetry generators annihilate all physical states (including the vacuum state), while at the same time, superpartners do not exist.

Quadratic Frequency Modulation Signals Parameter Estimation Based on Two-Dimensional Product Modified Parameterized Chirp Rate-Quadratic Chirp Rate Distribution.

PubMed

Qu, Zhiyu; Qu, Fuxin; Hou, Changbo; Jing, Fulong

2018-05-19

In an inverse synthetic aperture radar (ISAR) imaging system for targets with complex motion, the azimuth echo signals of the target are always modeled as multicomponent quadratic frequency modulation (QFM) signals. The chirp rate (CR) and quadratic chirp rate (QCR) estimation of QFM signals is very important to solve the ISAR image defocus problem. For multicomponent QFM (multi-QFM) signals, the conventional QR and QCR estimation algorithms suffer from the cross-term and poor anti-noise ability. This paper proposes a novel estimation algorithm called a two-dimensional product modified parameterized chirp rate-quadratic chirp rate distribution (2D-PMPCRD) for QFM signals parameter estimation. The 2D-PMPCRD employs a multi-scale parametric symmetric self-correlation function and modified nonuniform fast Fourier transform-Fast Fourier transform to transform the signals into the chirp rate-quadratic chirp rate (CR-QCR) domains. It can greatly suppress the cross-terms while strengthening the auto-terms by multiplying different CR-QCR domains with different scale factors. Compared with high order ambiguity function-integrated cubic phase function and modified Lv's distribution, the simulation results verify that the 2D-PMPCRD acquires higher anti-noise performance and obtains better cross-terms suppression performance for multi-QFM signals with reasonable computation cost.

A Quadratic Spring Equation

ERIC Educational Resources Information Center

Fay, Temple H.

2010-01-01

Through numerical investigations, we study examples of the forced quadratic spring equation [image omitted]. By performing trial-and-error numerical experiments, we demonstrate the existence of stability boundaries in the phase plane indicating initial conditions yielding bounded solutions, investigate the resonance boundary in the [omega]…

On orthogonality preserving quadratic stochastic operators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mukhamedov, Farrukh; Taha, Muhammad Hafizuddin Mohd

2015-05-15

A quadratic stochastic operator (in short QSO) is usually used to present the time evolution of differing species in biology. Some quadratic stochastic operators have been studied by Lotka and Volterra. In the present paper, we first give a simple characterization of Volterra QSO in terms of absolutely continuity of discrete measures. Further, we introduce a notion of orthogonal preserving QSO, and describe such kind of operators defined on two dimensional simplex. It turns out that orthogonal preserving QSOs are permutations of Volterra QSO. The associativity of genetic algebras generated by orthogonal preserving QSO is studied too.

Osmolyte effects on helix formation in peptides and the stability of coiled-coils

PubMed Central

Celinski, Scott A.; Scholtz, J. Martin

2002-01-01

The ability of several naturally occurring substances known as osmolytes to induce helix formation in an alanine-based peptide have been investigated. As predicted by the osmophobic effect hypothesis, the osmolytes studies here do induce helix formation. Trimethylamine-N-oxide (TMAO) is the best structure-inducing osmolytes investigated here, but it is not as effective in promoting helix formation as the common cosolvent trifluoroethanol (TFE). We also provide a semiquantitative study of the ability of TMAO to induce helix formation and urea, which acts as a helix (and protein) denaturant. We find that on a molar basis, these agents are exactly counteractive as structure inducing and unfolding agents. Finally, we extend the investigations to the effects of urea and TMAO on the stability of a dimeric coiled-coil peptide and find identical results. Together these results support the tenets of the osmophobic hypothesis and highlight the importance of the polypeptide backbone in protein folding and stability. PMID:12142459

Basic helix-loop-helix transcription factors in evolution: Roles in development of mesoderm and neural tissues.

PubMed

Gyoja, Fuki

2017-09-01

Basic helix-loop-helix (bHLH) transcription factors have attracted the attention of developmental and evolutionary biologists for decades because of their conserved functions in mesodermal and neural tissue formation in both vertebrates and fruit flies. Their evolutionary history is of special interest because it will likely provide insights into developmental processes and refinement of metazoan-specific traits. This review briefly considers advances in developmental biological studies on bHLHs/HLHs. I also discuss recent genome-wide surveys and molecular phylogenetic analyses of these factors in a wide range of metazoans. I hypothesize that interactions between metazoan-specific Group A, D, and E bHLH/HLH factors enabled a sophisticated transition system from cell proliferation to differentiation in multicellular development. This control mechanism probably emerged initially to organize a multicellular animal body and was subsequently recruited to form evolutionarily novel tissues, which differentiated during a later ontogenetic phase. © 2017 Wiley Periodicals, Inc.

Advanced Nonlinear Latent Variable Modeling: Distribution Analytic LMS and QML Estimators of Interaction and Quadratic Effects

ERIC Educational Resources Information Center

Kelava, Augustin; Werner, Christina S.; Schermelleh-Engel, Karin; Moosbrugger, Helfried; Zapf, Dieter; Ma, Yue; Cham, Heining; Aiken, Leona S.; West, Stephen G.

2011-01-01

Interaction and quadratic effects in latent variable models have to date only rarely been tested in practice. Traditional product indicator approaches need to create product indicators (e.g., x[superscript 2] [subscript 1], x[subscript 1]x[subscript 4]) to serve as indicators of each nonlinear latent construct. These approaches require the use of…

A basic helix-loop-helix transcription factor, PhFBH4, regulates flower senescence by modulating ethylene biosynthesis pathway in petunia.

PubMed

Yin, Jing; Chang, Xiaoxiao; Kasuga, Takao; Bui, Mai; Reid, Michael S; Jiang, Cai-Zhong

2015-01-01

The basic helix-loop-helix (bHLH) transcription factors (TFs) play important roles in regulating multiple biological processes in plants. However, there are few reports about the function of bHLHs in flower senescence. In this study, a bHLH TF, PhFBH4, was found to be dramatically upregulated during flower senescence. Transcription of PhFBH4 is induced by plant hormones and abiotic stress treatments. Silencing of PhFBH4 using virus-induced gene silencing or an antisense approach extended flower longevity, while transgenic petunia flowers with an overexpression construct showed a reduction in flower lifespan. Abundance of transcripts of senescence-related genes (SAG12, SAG29) was significantly changed in petunia PhFBH4 transgenic flowers. Furthermore, silencing or overexpression of PhFBH4 reduced or increased, respectively, transcript abundances of important ethylene biosynthesis-related genes, ACS1 and ACO1, thereby influencing ethylene production. An electrophoretic mobility shift assay showed that the PhFBH4 protein physically interacted with the G-box cis-element in the promoter of ACS1, suggesting that ACS1 was a direct target of the PhFBH4 protein. In addition, ectopic expression of this gene altered plant development including plant height, internode length, and size of leaves and flowers, accompanied by alteration of transcript abundance of the gibberellin biosynthesis-related gene GA2OX3. Our results indicate that PhFBH4 plays an important role in regulating plant growth and development through modulating the ethylene biosynthesis pathway.

The Mystical "Quadratic Formula."

ERIC Educational Resources Information Center

March, Robert H.

1993-01-01

Uses projectile motion to explain the two roots found when using the quadratic formula. An example is provided for finding the time of flight for a projectile which has a negative root implying a negative time of flight. This negative time of flight also has a useful physical meaning. (MVL)

Linear quadratic optimization for positive LTI system

NASA Astrophysics Data System (ADS)

Muhafzan, Yenti, Syafrida Wirma; Zulakmal

2017-05-01

Nowaday the linear quadratic optimization subject to positive linear time invariant (LTI) system constitute an interesting study considering it can become a mathematical model of variety of real problem whose variables have to nonnegative and trajectories generated by these variables must be nonnegative. In this paper we propose a method to generate an optimal control of linear quadratic optimization subject to positive linear time invariant (LTI) system. A sufficient condition that guarantee the existence of such optimal control is discussed.

Alternative generation of well-aligned uniform lying helix texture in a cholesteric liquid crystal cell

NASA Astrophysics Data System (ADS)

Yu, Chia-Hua; Wu, Po-Chang; Lee, Wei

2017-10-01

This work demonstrates a simple approach for obtaining a well-aligned uniform lying helix (ULH) texture and a tri-bistable feature at ambient temperature in a typical 90°-twisted cell filled with a short-pitch cholesteric liquid crystal. This ULH texture is obtained at room temperature from initially field-induced helix-free homeotropic state by gradually decreasing the applied voltage. Depending on the way and rate of reducing the voltage, three stable states (i.e., Grandjean planar, focal conic, and ULH) are generated and switching between any two of them is realized. Moreover, the electrical operation of the cell in the ULH state enables the tunability in phase retardation via the deformation of the ULH. The observations made in this work may be useful for applications such as tunable phase modulators and energy-efficient photonic devices.

Modulating Transmembrane α-Helix Interactions through pH-Sensitive Boundary Residues.

PubMed

Ng, Derek P; Deber, Charles M

2016-08-09

Changes in pH can alter the structure and activity of proteins and may be used by the cell to control molecular function. This coupling can also be used in non-native applications through the design of pH-sensitive biomolecules. For example, the pH (low) insertion peptide (pHLIP) can spontaneously insert into a lipid bilayer when the pH decreases. We have previously shown that the α-helicity and helix-helix interactions of the TM2 α-helix of the proteolipid protein (PLP) are sensitive to the local hydrophobicity at its C-terminus. Given that there is an ionizable residue (Glu-88) at the C-terminus of this transmembrane (TM) segment, we hypothesized that changing the ionization state of this residue through pH may alter the local hydrophobicity of the peptide enough to affect both its secondary structure and helix-helix interactions. To examine this phenomenon, we synthesized peptide analogues of the PLP TM2 α-helix (wild-type sequence (66)AFQYVIYGTASFFFLYGALLLAEGF(90)). Using circular dichroism and Förster resonance energy transfer in the membrane-mimetic detergent sodium dodecyl sulfate, we found that a decrease in pH increases both peptide α-helicity and the extent of self-association. This pH-dependent effect is due specifically to the presence of Glu-88 at the C-terminus. Additional experiments in which Phe-90 was mutated to residues of varying hydrophobicities indicated that the strength of this effect is dependent on the local hydrophobicity near Glu-88. Our results have implications for the design of TM peptide switches and improve our understanding of how membrane protein structure and activity can be regulated through local molecular environmental changes.

Visualising the Roots of Quadratic Equations with Complex Coefficients

ERIC Educational Resources Information Center

Bardell, Nicholas S.

2014-01-01

This paper is a natural extension of the root visualisation techniques first presented by Bardell (2012) for quadratic equations with real coefficients. Consideration is now given to the familiar quadratic equation "y = ax[superscript 2] + bx + c" in which the coefficients "a," "b," "c" are generally…

Scaling Laws for the Multidimensional Burgers Equation with Quadratic External Potential

NASA Astrophysics Data System (ADS)

Leonenko, N. N.; Ruiz-Medina, M. D.

2006-07-01

The reordering of the multidimensional exponential quadratic operator in coordinate-momentum space (see X. Wang, C.H. Oh and L.C. Kwek (1998). J. Phys. A.: Math. Gen. 31:4329-4336) is applied to derive an explicit formulation of the solution to the multidimensional heat equation with quadratic external potential and random initial conditions. The solution to the multidimensional Burgers equation with quadratic external potential under Gaussian strongly dependent scenarios is also obtained via the Hopf-Cole transformation. The limiting distributions of scaling solutions to the multidimensional heat and Burgers equations with quadratic external potential are then obtained under such scenarios.

Observational constraints on cosmological models with Chaplygin gas and quadratic equation of state

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharov, G.S., E-mail: german.sharov@mail.ru

Observational manifestations of accelerated expansion of the universe, in particular, recent data for Type Ia supernovae, baryon acoustic oscillations, for the Hubble parameter H ( z ) and cosmic microwave background constraints are described with different cosmological models. We compare the ΛCDM, the models with generalized and modified Chaplygin gas and the model with quadratic equation of state. For these models we estimate optimal model parameters and their permissible errors with different approaches to calculation of sound horizon scale r {sub s} ( z {sub d} ). Among the considered models the best value of χ{sup 2} is achieved formore » the model with quadratic equation of state, but it has 2 additional parameters in comparison with the ΛCDM and therefore is not favored by the Akaike information criterion.« less

Val-->Ala mutations selectively alter helix-helix packing in the transmembrane segment of phage M13 coat protein.

PubMed Central

Deber, C M; Khan, A R; Li, Z; Joensson, C; Glibowicka, M; Wang, J

1993-01-01

Val-->Ala mutations within the effective transmembrane segment of a model single-spanning membrane protein, the 50-residue major coat (gene VIII) protein of bacteriophage M13, are shown to have sequence-dependent impacts on stabilization of membrane-embedded helical dimeric structures. Randomized mutagenesis performed on the coat protein hydrophobic segment 21-39 (YIGYAWAMV-VVIVGATIGI) produced a library of viable mutants which included those in which each of the four valine residues was replaced by an alanine residue. Significant variations found among these Val-->Ala mutants in the relative populations and thermal stabilities of monomeric and dimeric helical species observed on SDS/PAGE, and in the range of their alpha-helix-->beta-sheet transition temperatures confirmed that intramembranous valine residues are not simply universal contributors to membrane anchoring. Additional analyses of (i) nonmutatable sites in the mutant protein library, (ii) the properties of the double mutant V29A-V31A obtained by recycling mutant V31A DNA through mutagenesis procedures, and (iii) energy-minimized helical dimer structures of wild-type and mutant V31A transmembrane regions indicated that the transmembrane hydrophobic core helix of the M13 coat protein can be partitioned into alternating pairs of potential protein-interactive residues (V30, V31; G34, A35; G38, I39) and membrane-interactive residues (M28, V29; I32, V33; T36, I37). The overall results consitute an experimental approach to categorizing the distinctive contributions to structure of the residues comprising a protein-protein packing interface vs. those facing lipid and confirm the sequence-dependent capacity of specific residues within the transmembrane domain to modulate protein-protein interactions which underlie regulatory events in membrane proteins. Images Fig. 2 Fig. 4 PMID:8265602

Val-->Ala mutations selectively alter helix-helix packing in the transmembrane segment of phage M13 coat protein.

PubMed

Deber, C M; Khan, A R; Li, Z; Joensson, C; Glibowicka, M; Wang, J

1993-12-15

Val-->Ala mutations within the effective transmembrane segment of a model single-spanning membrane protein, the 50-residue major coat (gene VIII) protein of bacteriophage M13, are shown to have sequence-dependent impacts on stabilization of membrane-embedded helical dimeric structures. Randomized mutagenesis performed on the coat protein hydrophobic segment 21-39 (YIGYAWAMV-VVIVGATIGI) produced a library of viable mutants which included those in which each of the four valine residues was replaced by an alanine residue. Significant variations found among these Val-->Ala mutants in the relative populations and thermal stabilities of monomeric and dimeric helical species observed on SDS/PAGE, and in the range of their alpha-helix-->beta-sheet transition temperatures confirmed that intramembranous valine residues are not simply universal contributors to membrane anchoring. Additional analyses of (i) nonmutatable sites in the mutant protein library, (ii) the properties of the double mutant V29A-V31A obtained by recycling mutant V31A DNA through mutagenesis procedures, and (iii) energy-minimized helical dimer structures of wild-type and mutant V31A transmembrane regions indicated that the transmembrane hydrophobic core helix of the M13 coat protein can be partitioned into alternating pairs of potential protein-interactive residues (V30, V31; G34, A35; G38, I39) and membrane-interactive residues (M28, V29; I32, V33; T36, I37). The overall results consitute an experimental approach to categorizing the distinctive contributions to structure of the residues comprising a protein-protein packing interface vs. those facing lipid and confirm the sequence-dependent capacity of specific residues within the transmembrane domain to modulate protein-protein interactions which underlie regulatory events in membrane proteins.

A reduced successive quadratic programming strategy for errors-in-variables estimation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tjoa, I.-B.; Biegler, L. T.; Carnegie-Mellon Univ.

Parameter estimation problems in process engineering represent a special class of nonlinear optimization problems, because the maximum likelihood structure of the objective function can be exploited. Within this class, the errors in variables method (EVM) is particularly interesting. Here we seek a weighted least-squares fit to the measurements with an underdetermined process model. Thus, both the number of variables and degrees of freedom available for optimization increase linearly with the number of data sets. Large optimization problems of this type can be particularly challenging and expensive to solve because, for general-purpose nonlinear programming (NLP) algorithms, the computational effort increases atmore » least quadratically with problem size. In this study we develop a tailored NLP strategy for EVM problems. The method is based on a reduced Hessian approach to successive quadratic programming (SQP), but with the decomposition performed separately for each data set. This leads to the elimination of all variables but the model parameters, which are determined by a QP coordination step. In this way the computational effort remains linear in the number of data sets. Moreover, unlike previous approaches to the EVM problem, global and superlinear properties of the SQP algorithm apply naturally. Also, the method directly incorporates inequality constraints on the model parameters (although not on the fitted variables). This approach is demonstrated on five example problems with up to 102 degrees of freedom. Compared to general-purpose NLP algorithms, large improvements in computational performance are observed.« less

Regulation of TCF ETS-domain transcription factors by helix-loop-helix motifs.

PubMed

Stinson, Julie; Inoue, Toshiaki; Yates, Paula; Clancy, Anne; Norton, John D; Sharrocks, Andrew D

2003-08-15

DNA binding by the ternary complex factor (TCF) subfamily of ETS-domain transcription factors is tightly regulated by intramolecular and intermolecular interactions. The helix-loop-helix (HLH)-containing Id proteins are trans-acting negative regulators of DNA binding by the TCFs. In the TCF, SAP-2/Net/ERP, intramolecular inhibition of DNA binding is promoted by the cis-acting NID region that also contains an HLH-like motif. The NID also acts as a transcriptional repression domain. Here, we have studied the role of HLH motifs in regulating DNA binding and transcription by the TCF protein SAP-1 and how Cdk-mediated phosphorylation affects the inhibitory activity of the Id proteins towards the TCFs. We demonstrate that the NID region of SAP-1 is an autoinhibitory motif that acts to inhibit DNA binding and also functions as a transcription repression domain. This region can be functionally replaced by fusion of Id proteins to SAP-1, whereby the Id moiety then acts to repress DNA binding in cis. Phosphorylation of the Ids by cyclin-Cdk complexes results in reduction in protein-protein interactions between the Ids and TCFs and relief of their DNA-binding inhibitory activity. In revealing distinct mechanisms through which HLH motifs modulate the activity of TCFs, our results therefore provide further insight into the role of HLH motifs in regulating TCF function and how the inhibitory properties of the trans-acting Id HLH proteins are themselves regulated by phosphorylation.

A Sequential Linear Quadratic Approach for Constrained Nonlinear Optimal Control with Adaptive Time Discretization and Application to Higher Elevation Mars Landing Problem

NASA Astrophysics Data System (ADS)

Sandhu, Amit

A sequential quadratic programming method is proposed for solving nonlinear optimal control problems subject to general path constraints including mixed state-control and state only constraints. The proposed algorithm further develops on the approach proposed in [1] with objective to eliminate the use of a high number of time intervals for arriving at an optimal solution. This is done by introducing an adaptive time discretization to allow formation of a desirable control profile without utilizing a lot of intervals. The use of fewer time intervals reduces the computation time considerably. This algorithm is further used in this thesis to solve a trajectory planning problem for higher elevation Mars landing.

Comparison of the quadratic configuration interaction and coupled cluster approaches to electron correlation including the effect of triple excitations

NASA Technical Reports Server (NTRS)

Taylor, Peter R.; Lee, Timothy J.; Rendell, Alistair P.

1990-01-01

The recently proposed quadratic configuration interaction (QCI) method is compared with the more rigorous coupled cluster (CC) approach for a variety of chemical systems. Some of these systems are well represented by a single-determinant reference function and others are not. The finite order singles and doubles correlation energy, the perturbational triples correlation energy, and a recently devised diagnostic for estimating the importance of multireference effects are considered. The spectroscopic constants of CuH, the equilibrium structure of cis-(NO)2 and the binding energies of Be3, Be4, Mg3, and Mg4 were calculated using both approaches. The diagnostic for estimating multireference character clearly demonstrates that the QCI method becomes less satisfactory than the CC approach as non-dynamical correlation becomes more important, in agreement with a perturbational analysis of the two methods and the numerical estimates of the triple excitation energies they yield. The results for CuH show that the differences between the two methods become more apparent as the chemical systems under investigation becomes more multireference in nature and the QCI results consequently become less reliable. Nonetheless, when the system of interest is dominated by a single reference determinant both QCI and CC give very similar results.

Inhibition of Bacterial Rna Polymerase by Streptolydigin: Stabilization of A Straight-Bridge-Helix Active-Center Conformation

PubMed Central

Tuske, Steven; Sarafianos, Stefan G.; Wang, Xinyue; Hudson, Brian; Sineva, Elena; Mukhopadhyay, Jayanta; Birktoft, Jens J.; Leroy, Olivier; Ismail, Sajida; Clark, Arthur D.; Dharia, Chhaya; Napoli, Andrew; Laptenko, Oleg; Lee, Jookyung; Borukhov, Sergei; Ebright, Richard H.; Arnold, Eddy

2009-01-01

We define the target, mechanism, and structural basis of inhibition of bacterial RNA polymerase (RNAP) by the tetramic-acid antibiotic streptolydigin (Stl). Stl binds to a site adjacent to, but not overlapping, the RNAP active center and stabilizes an RNAP-active-center conformational state with a straight bridge helix. The results provide direct support for the proposals that alternative straight-bridge-helix and bent-bridge-helix RNAP-active-center conformations exist, and that cycling between straight-bridge-helix and bent-bridge-helix RNAP-active-center conformations is required for RNAP function. The results set bounds on models for RNAP function and suggest strategies for design of novel antibacterial agents. PMID:16122422

The grape berry-specific basic helix-loop-helix transcription factor VvCEB1 affects cell size.

PubMed

Nicolas, Philippe; Lecourieux, David; Gomès, Eric; Delrot, Serge; Lecourieux, Fatma

2013-02-01

The development of fleshy fruits involves complex physiological and biochemical changes. After fertilization, fruit growth usually begins with cell division, continues with both cell division and expansion, allowing fruit set to occur, and ends with cell expansion only. In spite of the economical importance of grapevine, the molecular mechanisms controlling berry growth are not fully understood. The present work identified and characterized Vitis vinifera cell elongation bHLH protein (VvCEB1), a basic helix-loop-helix (bHLH) transcription factor controlling cell expansion in grape. VvCEB1 was expressed specifically in berry-expanding tissues with a maximum around veraison. The study of VvCEB1 promoter activity in tomato confirmed its specific fruit expression during the expansion phase. Overexpression of VvCEB1 in grape embryos showed that this protein stimulates cell expansion and affects the expression of genes involved in cell expansion, including genes of auxin metabolism and signalling. Taken together, these data show that VvCEB1 is a fruit-specific bHLH transcription factor involved in grape berry development.

An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network

PubMed Central

Holden, Brian J; Pinney, John W; Lovell, Simon C; Amoutzias, Grigoris D; Robertson, David L

2007-01-01

Background Alternative representations of biochemical networks emphasise different aspects of the data and contribute to the understanding of complex biological systems. In this study we present a variety of automated methods for visualisation of a protein-protein interaction network, using the basic helix-loop-helix (bHLH) family of transcription factors as an example. Results Network representations that arrange nodes (proteins) according to either continuous or discrete information are investigated, revealing the existence of protein sub-families and the retention of interactions following gene duplication events. Methods of network visualisation in conjunction with a phylogenetic tree are presented, highlighting the evolutionary relationships between proteins, and clarifying the context of network hubs and interaction clusters. Finally, an optimisation technique is used to create a three-dimensional layout of the phylogenetic tree upon which the protein-protein interactions may be projected. Conclusion We show that by incorporating secondary genomic, functional or phylogenetic information into network visualisation, it is possible to move beyond simple layout algorithms based on network topology towards more biologically meaningful representations. These new visualisations can give structure to complex networks and will greatly help in interpreting their evolutionary origins and functional implications. Three open source software packages (InterView, TVi and OptiMage) implementing our methods are available. PMID:17683601

Analysis of Students' Error in Learning of Quadratic Equations

ERIC Educational Resources Information Center

Zakaria, Effandi; Ibrahim; Maat, Siti Mistima

2010-01-01

The purpose of the study was to determine the students' error in learning quadratic equation. The samples were 30 form three students from a secondary school in Jambi, Indonesia. Diagnostic test was used as the instrument of this study that included three components: factorization, completing the square and quadratic formula. Diagnostic interview…

Glass-like stress relaxation of a permanent gelatin network as a signature of pretransitional helix-coil fluctuations

NASA Astrophysics Data System (ADS)

Caroli, Christiane; Ronsin, Olivier; Lemaître, Anaël

2018-02-01

The stress response of permanently crosslinked gelatin gels was recently observed to display glass-like features, namely, a stretched-exponential behavior terminated by an exponential decay, the characteristic time scales of which increase dramatically with decreasing temperature. This phenomenon is studied here using a model of flexible polymer gel network where relaxation proceeds via elementary monomer exchanges between helix and coil segments. The relaxation dynamics of a full network simulation is found to be nearly identical to that of a model of independent strands, which shows that for flexible polymer gels in the range of elastic moduli of interest, both strand contour length disorder and elastic couplings are irrelevant. We thus focus on the independent strand model and find it not only to explain the observed functional form of the stress relaxation curves but also to yield predictions that match very satisfactorily the experimental measurements of final relaxation time and total stress drop. The system under study thus constitutes a rare case where the origin of glass-like behavior can be unambiguously identified, namely, as the signature of the enhancement of helix content fluctuations when approaching from above the mean-field helix-coil transition of strands.

Structural and functional aspects of winged-helix domains at the core of transcription initiation complexes.

PubMed

Teichmann, Martin; Dumay-Odelot, Hélène; Fribourg, Sébastien

2012-01-01

The winged helix (WH) domain is found in core components of transcription systems in eukaryotes and prokaryotes. It represents a sub-class of the helix-turn-helix motif. The WH domain participates in establishing protein-DNA and protein-protein-interactions. Here, we discuss possible explanations for the enrichment of this motif in transcription systems.

Exploring the membrane fusion mechanism through force-induced disassembly of HIV-1 six-helix bundle

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Kai; Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101; University of Chinese Academy of Sciences, Beijing 100049

Enveloped virus, such as HIV-1, employs membrane fusion mechanism to invade into host cell. HIV-1 gp41 ectodomain uses six-helix bundle configuration to accomplish this process. Using molecular dynamic simulations, we confirmed the stability of this six-helix bundle by showing high occupancy of hydrogen bonds and hydrophobic interactions. Key residues and interactions important for the bundle integration were characterized by force-induced unfolding simulations of six-helix bundle, exhibiting the collapse order of these groups of interactions. Moreover, our results in some way concerted with a previous theory that the formation of coiled-coil choose a route which involved cooperative interactions between the N-terminalmore » and C-terminal helix. -- Highlights: •Unfolding of HIV-1 gp41 six-helix bundle is studied by molecular dynamics simulations. •Specific interactions responsible for the stability of HIV-1 envelope post-fusion conformation were identified. •The gp41 six-helix bundle transition inducing membrane fusion might be a cooperative process of the three subunits.« less

Magnetic structure and magnetization of helical antiferromagnets in high magnetic fields perpendicular to the helix axis at zero temperature

DOE PAGES

Johnston, David

2017-09-05

The zero-temperature angles of magnetic moments in a helix or sinusoidal fan confined to the x y plane, with respect to an in-plane magnetic field H x applied perpendicular to the z axis of a helix or fan, are calculated for commensurate helices and fans with field-independent turn angles k d between moments in adjacent layers of the helix or fan using the classical J 0 - J 1 - J 2 Heisenberg model. For 0 < k d < 4 π / 9 , first-order transitions from helix to a fan structure occur at fields H t as previouslymore » inferred, where the fan is found to be approximately sinusoidal. However, for 4 π / 9 ≤ k d ≤ π , different behaviors are found depending on the value of k d and these properties vary nonmonotonically with k d . In this k d range, the change from helix to fanlike structure is usually a crossover with no phase transition between them, although first-order transitions are found for k d = 3 π / 5 and 8 π / 11 and a second-order transition for k d = 3 π / 4 . At a critical field H c , the fan or fanlike structures exhibit a second-order transition to the paramagnetic state. The H c for a helix undergoing a field-induced change to a fan or fanlike structure is found to be the same as for a sinusoidal fan with the same k d and interlayer interactions. We present analytical expressions for H c versus k d. We also calculated the average x -axis moment per spin μ x ave versus H x for helices and fans with crossovers and phase transitions between them. When smooth helix to fanlike crossovers occur in the range 4 π / 9 ≤ k d ≤ π , μ x ave exhibits an S-shape behavior with increasing H x . The behavior we predict is consistent with μ x ave ( H x ) data previously reported by Sangeetha et al. [Phys. Rev. B 94, 014422 (2016)] for single-crystal EuCo 2 P 2 possessing a helix ground state with k d ≈ 0.85 π . The low-field magnetic susceptibility and the ratio H t / H c are calculated analytically or numerically versus k d for helices, and are

Magnetic structure and magnetization of helical antiferromagnets in high magnetic fields perpendicular to the helix axis at zero temperature

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnston, David

The zero-temperature angles of magnetic moments in a helix or sinusoidal fan confined to the x y plane, with respect to an in-plane magnetic field H x applied perpendicular to the z axis of a helix or fan, are calculated for commensurate helices and fans with field-independent turn angles k d between moments in adjacent layers of the helix or fan using the classical J 0 - J 1 - J 2 Heisenberg model. For 0 < k d < 4 π / 9 , first-order transitions from helix to a fan structure occur at fields H t as previouslymore » inferred, where the fan is found to be approximately sinusoidal. However, for 4 π / 9 ≤ k d ≤ π , different behaviors are found depending on the value of k d and these properties vary nonmonotonically with k d . In this k d range, the change from helix to fanlike structure is usually a crossover with no phase transition between them, although first-order transitions are found for k d = 3 π / 5 and 8 π / 11 and a second-order transition for k d = 3 π / 4 . At a critical field H c , the fan or fanlike structures exhibit a second-order transition to the paramagnetic state. The H c for a helix undergoing a field-induced change to a fan or fanlike structure is found to be the same as for a sinusoidal fan with the same k d and interlayer interactions. We present analytical expressions for H c versus k d. We also calculated the average x -axis moment per spin μ x ave versus H x for helices and fans with crossovers and phase transitions between them. When smooth helix to fanlike crossovers occur in the range 4 π / 9 ≤ k d ≤ π , μ x ave exhibits an S-shape behavior with increasing H x . The behavior we predict is consistent with μ x ave ( H x ) data previously reported by Sangeetha et al. [Phys. Rev. B 94, 014422 (2016)] for single-crystal EuCo 2 P 2 possessing a helix ground state with k d ≈ 0.85 π . The low-field magnetic susceptibility and the ratio H t / H c are calculated analytically or numerically versus k d for helices, and are

Self-accelerating parabolic beams in quadratic nonlinear media

NASA Astrophysics Data System (ADS)

Dolev, Ido; Libster, Ana; Arie, Ady

2012-09-01

We present experimental observation of self-accelerating parabolic beams in quadratic nonlinear media. We show that the intensity peaks of the first and second harmonics are asynchronous with respect to one another in the two transverse coordinates. In addition, the two coupled harmonics have the same acceleration within and after the nonlinear medium. We also study the evolution of second harmonic accelerating beams inside the quadratic media and their correlation with theoretical beams.

Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides.

PubMed

Best, Robert B; Hummer, Gerhard

2009-07-02

Obtaining the correct balance of secondary structure propensities is a central priority in protein force-field development. Given that current force fields differ significantly in their alpha-helical propensities, a correction to match experimental results would be highly desirable. We have determined simple backbone energy corrections for two force fields to reproduce the fraction of helix measured in short peptides at 300 K. As validation, we show that the optimized force fields produce results in excellent agreement with nuclear magnetic resonance experiments for folded proteins and short peptides not used in the optimization. However, despite the agreement at ambient conditions, the dependence of the helix content on temperature is too weak, a problem shared with other force fields. A fit of the Lifson-Roig helix-coil theory shows that both the enthalpy and entropy of helix formation are too small: the helix extension parameter w agrees well with experiment, but its entropic and enthalpic components are both only about half the respective experimental estimates. Our structural and thermodynamic analyses point toward the physical origins of these shortcomings in current force fields, and suggest ways to address them in future force-field development.

The application of quadratic optimal cooperative control synthesis to a CH-47 helicopter

NASA Technical Reports Server (NTRS)

Townsend, Barbara K.

1987-01-01

A control-system design method, quadratic optimal cooperative control synthesis (CCS), is applied to the design of a stability and control augmentation system (SCAS). The CCS design method is different from other design methods in that it does not require detailed a priori design criteria, but instead relies on an explicit optimal pilot-model to create desired performance. The design method, which was developed previously for fixed-wing aircraft, is simplified and modified for application to a Boeing CH-47 helicopter. Two SCAS designs are developed using the CCS design methodology. The resulting CCS designs are then compared with designs obtained using classical/frequency-domain methods and linear quadratic regulator (LQR) theory in a piloted fixed-base simulation. Results indicate that the CCS method, with slight modifications, can be used to produce controller designs which compare favorably with the frequency-domain approach.

The application of quadratic optimal cooperative control synthesis to a CH-47 helicopter

NASA Technical Reports Server (NTRS)

Townsend, Barbara K.

1986-01-01

A control-system design method, Quadratic Optimal Cooperative Control Synthesis (CCS), is applied to the design of a Stability and Control Augmentation Systems (SCAS). The CCS design method is different from other design methods in that it does not require detailed a priori design criteria, but instead relies on an explicit optimal pilot-model to create desired performance. The design model, which was developed previously for fixed-wing aircraft, is simplified and modified for application to a Boeing Vertol CH-47 helicopter. Two SCAS designs are developed using the CCS design methodology. The resulting CCS designs are then compared with designs obtained using classical/frequency-domain methods and Linear Quadratic Regulator (LQR) theory in a piloted fixed-base simulation. Results indicate that the CCS method, with slight modifications, can be used to produce controller designs which compare favorably with the frequency-domain approach.

Quadratic genetic modifications: a streamlined route to cosmological simulations with controlled merger history

NASA Astrophysics Data System (ADS)

Rey, Martin P.; Pontzen, Andrew

2018-02-01

Recent work has studied the interplay between a galaxy's history and its observable properties using `genetically modified' cosmological zoom simulations. The approach systematically generates alternative histories for a halo, while keeping its cosmological environment fixed. Applications to date altered linear properties of the initial conditions, such as the mean overdensity of specified regions; we extend the formulation to include quadratic features, such as local variance, that determines the overall importance of smooth accretion relative to mergers in a galaxy's history. We introduce an efficient algorithm for this new class of modification and demonstrate its ability to control the variance of a region in a one-dimensional toy model. Outcomes of this work are twofold: (i) a clarification of the formulation of genetic modifications and (ii) a proof of concept for quadratic modifications leading the way to a forthcoming implementation in cosmological simulations.

Binary Inspiral in Quadratic Gravity

NASA Astrophysics Data System (ADS)

Yagi, Kent

2015-01-01

Quadratic gravity is a general class of quantum-gravity-inspired theories, where the Einstein-Hilbert action is extended through the addition of all terms quadratic in the curvature tensor coupled to a scalar field. In this article, we focus on the scalar Gauss- Bonnet (sGB) theory and consider the black hole binary inspiral in this theory. By applying the post-Newtonian (PN) formalism, we found that there is a scalar dipole radiation which leads to -1PN correction in the energy flux relative to gravitational radiation in general relativity. From the orbital decay rate of a low-mass X-ray binary A0600-20, we obtain the bound that is six orders of magnitude stronger than the current solar system bound. Furthermore, we show that the excess in the orbital decay rate of XTE J1118+480 can be explained by the scalar radiation in sGB theory.

Rotational strength of dye-helix complexes as studied by a potential model theory

NASA Astrophysics Data System (ADS)

Kamiya, Mamoru

1988-03-01

The fundamental features of the induced optical activity in dye-helix complexes are clarified by the trap potential model. The effect of the potential depth on the induced rotational strength is explained in terms of the relative magnitudes of the wave-phase and helix-phase variations in the path of an electron moving along a restricted helix segment just like an exciton trapped around a dye intercalation site. The potential parameters have been optimized so as to reproduce the ionic strength effect upon the rotational strengths induced in proflavine-DNA intercalation complexes.

Tangent Lines without Derivatives for Quadratic and Cubic Equations

ERIC Educational Resources Information Center

Carroll, William J.

2009-01-01

In the quadratic equation, y = ax[superscript 2] + bx + c, the equation y = bx + c is identified as the equation of the line tangent to the parabola at its y-intercept. This is extended to give a convenient method of graphing tangent lines at any point on the graph of a quadratic or a cubic equation. (Contains 5 figures.)

Sketching the General Quadratic Equation Using Dynamic Geometry Software

ERIC Educational Resources Information Center

Stols, G. H.

2005-01-01

This paper explores a geometrical way to sketch graphs of the general quadratic in two variables with Geometer's Sketchpad. To do this, a geometric procedure as described by De Temple is used, bearing in mind that this general quadratic equation (1) represents all the possible conics (conics sections), and the fact that five points (no three of…

Helix Nebula - the Science Cloud: a public-private partnership to build a multidisciplinary cloud platform for data intensive science

NASA Astrophysics Data System (ADS)

Jones, Bob; Casu, Francesco

2013-04-01

The feasibility of using commercial cloud services for scientific research is of great interest to research organisations such as CERN, ESA and EMBL, to the suppliers of cloud-based services and to the national and European funding agencies. Through the Helix Nebula - the Science Cloud [1] initiative and with the support of the European Commission, these stakeholders are driving a two year pilot-phase during which procurement processes and governance issues for a framework of public/private partnership will be appraised. Three initial flagship use cases from high energy physics, molecular biology and earth-observation are being used to validate the approach, enable a cost-benefit analysis to be undertaken and prepare the next stage of the Science Cloud Strategic Plan [2] to be developed and approved. The power of Helix Nebula lies in a shared set of services for initially 3 very different sciences each supporting a global community and thus building a common e-Science platform. Of particular relevance is the ESA sponsored flagship application SuperSites Exploitation Platform (SSEP [3]) that offers the global geo-hazard community a common platform for the correlation and processing of observation data for supersites monitoring. The US-NSF Earth Cube [4] and Ocean Observatory Initiative [5] (OOI) are taking a similar approach for data intensive science. The work of Helix Nebula and its recent architecture model [6] has shown that is it technically feasible to allow publicly funded infrastructures, such as EGI [7] and GEANT [8], to interoperate with commercial cloud services. Such hybrid systems are in the interest of the existing users of publicly funded infrastructures and funding agencies because they will provide "freedom of choice" over the type of computing resources to be consumed and the manner in which they can be obtained. But to offer such freedom-of choice across a spectrum of suppliers, various issues such as intellectual property, legal responsibility

Selection of a platinum-binding sequence in a loop of a four-helix bundle protein.

PubMed

Yagi, Sota; Akanuma, Satoshi; Kaji, Asumi; Niiro, Hiroya; Akiyama, Hayato; Uchida, Tatsuya; Yamagishi, Akihiko

2018-02-01

Protein-metal hybrids are functional materials with various industrial applications. For example, a redox enzyme immobilized on a platinum electrode is a key component of some biofuel cells and biosensors. To create these hybrid materials, protein molecules are bound to metal surfaces. Here, we report the selection of a novel platinum-binding sequence in a loop of a four-helix bundle protein, the Lac repressor four-helix protein (LARFH), an artificial protein in which four identical α-helices are connected via three identical loops. We created a genetic library in which the Ser-Gly-Gln-Gly-Gly-Ser sequence within the first inter-helical loop of LARFH was semi-randomly mutated. The library was then subjected to selection for platinum-binding affinity by using the T7 phage display method. The majority of the selected variants contained the Tyr-Lys-Arg-Gly-Tyr-Lys (YKRGYK) sequence in their randomized segment. We characterized the platinum-binding properties of mutant LARFH by using quartz crystal microbalance analysis. Mutant LARFH seemed to interact with platinum through its loop containing the YKRGYK sequence, as judged by the estimated exclusive area occupied by a single molecule. Furthermore, a 10-residue peptide containing the YKRGYK sequence bound to platinum with reasonably high affinity and basic side chains in the peptide were crucial in mediating this interaction. In conclusion, we have identified an amino acid sequence, YKRGYK, in the loop of a helix-loop-helix motif that shows high platinum-binding affinity. This sequence could be grafted into loops of other polypeptides as an approach to immobilize proteins on platinum electrodes for use as biosensors among other applications. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Evolution of the α-Subunit of Na/K-ATPase from Paramecium to Homo sapiens: Invariance of Transmembrane Helix Topology.

PubMed

Morrill, Gene A; Kostellow, Adele B; Liu, Lijun; Gupta, Raj K; Askari, Amir

2016-05-01

Na/K-ATPase is a key plasma membrane enzyme involved in cell signaling, volume regulation, and maintenance of electrochemical gradients. The α-subunit, central to these functions, belongs to a large family of P-type ATPases. Differences in transmembrane (TM) helix topology, sequence homology, helix-helix contacts, cell signaling, and protein domains of Na/K-ATPase α-subunit were compared in fungi (Beauveria), unicellular organisms (Paramecia), primitive multicellular organisms (Hydra), and vertebrates (Xenopus, Homo sapiens), and correlated with evolution of physiological functions in the α-subunit. All α-subunits are of similar length, with groupings of four and six helices in the N- and C-terminal regions, respectively. Minimal homology was seen for protein domain patterns in Paramecium and Hydra, with high correlation between Hydra and vertebrates. Paramecium α-subunits display extensive disorder, with minimal helix contacts. Increases in helix contacts in Hydra approached vertebrates. Protein motifs known to be associated with membrane lipid rafts and cell signaling reveal significant positional shifts between Paramecium and Hydra vulgaris, indicating that regional membrane fluidity changes occur during evolution. Putative steroid binding sites overlapping TM-3 occurred in all species. Sites associated with G-protein-receptor stimulation occur both in vertebrates and amphibia but not in Hydra or Paramecia. The C-terminus moiety "KETYY," necessary for the Na(+) activation of pump phosphorylation, is not present in unicellular species indicating the absence of classical Na(+)/K(+)-pumps. The basic protein topology evolved earliest, followed by increases in protein domains and ordered helical arrays, correlated with appearance of α-subunit regions known to involve cell signaling, membrane recycling, and ion channel formation.

Symmetric quadratic Hamiltonians with pseudo-Hermitian matrix representation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fernández, Francisco M., E-mail: fernande@quimica.unlp.edu.ar

2016-06-15

We prove that any symmetric Hamiltonian that is a quadratic function of the coordinates and momenta has a pseudo-Hermitian adjoint or regular matrix representation. The eigenvalues of the latter matrix are the natural frequencies of the Hamiltonian operator. When all the eigenvalues of the matrix are real, then the spectrum of the symmetric Hamiltonian is real and the operator is Hermitian. As illustrative examples we choose the quadratic Hamiltonians that model a pair of coupled resonators with balanced gain and loss, the electromagnetic self-force on an oscillating charged particle and an active LRC circuit. -- Highlights: •Symmetric quadratic operators aremore » useful models for many physical applications. •Any such operator exhibits a pseudo-Hermitian matrix representation. •Its eigenvalues are the natural frequencies of the Hamiltonian operator. •The eigenvalues may be real or complex and describe a phase transition.« less

Helix A Stabilization Precedes Amino-terminal Lobe Activation upon Calcium Binding to Calmodulin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Baowei; Lowry, David; Mayer, M. Uljana

2008-08-09

The structural coupling between opposing domains of CaM was investigated using the conformationally sensitive biarsenical probe 4,5-bis(1,3,2-dithioarsolan-2-yl)-resorufin (ReAsH), which upon binding to an engineered tetracysteine binding motif near the end of helix A (Thr-5 to Phe-19) becomes highly fluorescent. Changes in conformation and dynamics are reflective of the native CaM structure, as there is no change in the 1H- 15N HSQC NMR spectrum in comparison to wild-type CaM. We find evidence of a conformational intermediate associated with CaM activation, where calcium occupancy of sites in the amino-terminal and carboxyl-terminal lobes of CaM differentially affect the fluorescence intensity of bound ReAsH.more » Insight into the structure of the conformational intermediate is possible from a consideration of calcium-dependent changes in rates of ReAsH binding and helix A mobility, which respectively distinguish secondary structural changes associated with helix A stabilization from the tertiary structural reorganization of the amino-terminal lobe of CaM necessary for high-affinity binding to target proteins. Helix A stabilization is associated with calcium occupancy of sites in the carboxyl-terminal lobe (Kd = 0.36 ± 0.04 μM), which results in a reduction in the rate of ReAsH binding from 4900 M -1 sec -1 to 370 M -1 sec -1. In comparison, tertiary structural changes involving helix A and other structural elements in the amino-terminal lobe requires calcium-occupancy of amino-terminal sites (Kd = 18 ± 3 μM). Observed secondary and tertiary structural changes involving helix A in response to the sequential calcium occupancy of carboxyl- and amino-terminal lobe calcium binding sites suggest an important involvement of helix A in mediating the structural coupling between the opposing domains of CaM. These results are discussed in terms of a model in which carboxyl-terminal lobe calcium activation induces secondary structural changes within the interdomain

Control of regulatory T cell and Th17 cell differentiation by inhibitory helix-loop-helix protein Id3

PubMed Central

Maruyama, Takashi; Li, Jun; Vaque, Jose P.; Konkel, Joanne E.; Wang, Weifeng; Zhang, Baojun; Zhang, Pin; Zamarron, Brian; Yu, Dongyang; Wu, Yuntao; Zhuang, Yuan; Gutkind, J. Silvio; Chen, WanJun

2010-01-01

The molecular mechanisms directing Foxp3 gene transcription in CD4+ T cells remain ill defined. We show that deletion of the inhibitory helix-loop-helix (HLH) protein Id3 results in defective Foxp3+ Treg cell generation. We identified two transforming grothw factor-β1 (TGF-β1)-dependent mechanisms that are vital for activation of Foxp3 gene transcription, and are defective in Id3−/− CD4+ T cells. Enhanced binding of the HLH protein E2A to the Foxp3 promoter promoted Foxp3 gene transcription. Id3 was required to relieve inhibition by GATA-3 at the Foxp3 promoter. Further, Id3−/− T cells increased differentiation of Th17 cells in vitro and in a mouse asthma model. A network of factors therefore act in a TGF-β-dependent manner to control Foxp3 expression and inhibit Th17 cell development. PMID:21131965

The Helix Nebula: Unraveling at the Seams

NASA Image and Video Library

2012-10-03

This image from NASA Spitzer and GALEX shows the Helix nebula, a dying star throwing a cosmic tantrum. In death, the star dusty outer layers are unraveling into space, glowing from the intense UV radiation being pumped out by the hot stellar core.

The CDRH Helix-I: a physical evaluation.

PubMed

Gopal, M K; Cetas, T C

1990-01-01

The use of a resonant helical coil with predominantly axial electric fields for regional hyperthermia in the abdomen and pelvis is addressed. The Helix-I applicator, which consists of a three-turn, 36-cm-long, oval-wound helical coil measuring 60 and 43 cm along its major and minor axes, respectively, is described, and specific absorption rate (SAR) measurements for the device are reported. Measurements of the E-field are also described. Specific absorption patterns for the Helix, determined by transient temperature measurements using a gel phantom, and by E(2)-field scans using a liquid phantom, are in general agreement. The general agreement of electric power intensity distribution, inside and outside the phantom, with corresponding SAR distributions obtained from transient temperature data, ensures reliability of the distribution patterns. The E(2) contours provide a clear picture of hot and cold spots as well as the nature of the general distribution.

One Peptide Reveals the Two Faces of α-Helix Unfolding-Folding Dynamics.

PubMed

Jesus, Catarina S H; Cruz, Pedro F; Arnaut, Luis G; Brito, Rui M M; Serpa, Carlos

2018-04-12

The understanding of fast folding dynamics of single α-helices comes mostly from studies on rationally designed peptides displaying sequences with high helical propensity. The folding/unfolding dynamics and energetics of α-helix conformations in naturally occurring peptides remains largely unexplored. Here we report the study of a protein fragment analogue of the C-peptide from bovine pancreatic ribonuclease-A, RN80, a 13-amino acid residue peptide that adopts a highly populated helical conformation in aqueous solution. 1 H NMR and CD structural studies of RN80 showed that α-helix formation displays a pH-dependent bell-shaped curve, with a maximum near pH 5, and a large decrease in helical content in alkaline pH. The main forces stabilizing this short α-helix were identified as a salt bridge formed between Glu-2 and Arg-10 and the cation-π interaction involving Tyr-8 and His-12. Thus, deprotonation of Glu-2 or protonation of His-12 are essential for the RN80 α-helix stability. In the present study, RN80 folding and unfolding were triggered by laser-induced pH jumps and detected by time-resolved photoacoustic calorimetry (PAC). The photoacid proton release, amino acid residue protonation, and unfolding/folding events occur at different time scales and were clearly distinguished using time-resolved PAC. The partial unfolding of the RN80 α-helix, due to protonation of Glu-2 and consequent breaking of the stabilizing salt bridge between Glu-2 and Arg-10, is characterized by a concentration-independent volume expansion in the sub-microsecond time range (0.8 mL mol -1 , 369 ns). This small volume expansion reports the cost of peptide backbone rehydration upon disruption of a solvent-exposed salt bridge, as well as backbone intrinsic expansion. On the other hand, RN80 α-helix folding triggered by His-12 protonation and subsequent formation of a cation-π interaction leads to a microsecond volume contraction (-6.0 mL mol -1 , ∼1.7 μs). The essential role of two

Mouse interleukin-2 structure-function studies: substitutions in the first alpha-helix can specifically inactivate p70 receptor binding and mutations in the fifth alpha-helix can specifically inactivate p55 receptor binding.

PubMed Central

Zurawski, S M; Zurawski, G

1989-01-01

The function of two alpha-helical regions of mouse interleukin-2 were analyzed by saturation substitution analysis. The functional parts of the first alpha-helix (A) was defined as residues 31-39 by the observation that proline substitutions within this region inactivate the protein. Four residues within alpha-helix A, Leu31, Asp34, Leu35 and Leu38, were found to be crucial for biological activity. Structural modeling suggested that these four residues are clustered on one face of alpha-helix A. Residues 31 and 35 had to remain hydrophobic for the molecule to be functional. At residue 38 there was a preference for hydrophobic side chain residues, while at residue 34 some small side chain residues as well as acidic or amide side chain residues were functionally acceptable. Inactivating changes at residue 34 had no effect upon the ability of the protein to interact with the p55 receptor. Disruption of the fifth alpha-helix (E), which had little effect upon biological activity, resulted in an inability of the protein to interact with the p55 receptor. Mutagenesis of the alpha-helix E region demonstrated that alpha-helicity and the nature of the side chain residues in this region were unimportant for biological activity. The region immediately proximal to alpha-helix E was important only for the single intramolecular disulfide linkage. PMID:2583124

Disruption of the LOV-Jalpha helix interaction activates phototropin kinase activity.

PubMed

Harper, Shannon M; Christie, John M; Gardner, Kevin H

2004-12-28

Light plays a crucial role in activating phototropins, a class of plant photoreceptors that are sensitive to blue and UV-A wavelengths. Previous studies indicated that phototropin uses a bound flavin mononucleotide (FMN) within its light-oxygen-voltage (LOV) domain to generate a protein-flavin covalent bond under illumination. In the C-terminal LOV2 domain of Avena sativa phototropin 1, formation of this bond triggers a conformational change that results in unfolding of a helix external to this domain called Jalpha [Harper, S. M., et al. (2003) Science 301, 1541-1545]. Though the structural effects of illumination were characterized, it was unknown how these changes are coupled to kinase activation. To examine this, we made a series of point mutations along the Jalpha helix to disrupt its interaction with the LOV domain in a manner analogous to light activation. Using NMR spectroscopy and limited proteolysis, we demonstrate that several of these mutations displace the Jalpha helix from the LOV domain independently of illumination. When placed into the full-length phototropin protein, these point mutations display constitutive kinase activation, without illumination of the sample. These results indicate that unfolding of the Jalpha helix is the critical event in regulation of kinase signaling for the phototropin proteins.

Structure of bacteriophage [phi]29 head fibers has a supercoiled triple repeating helix-turn-helix motif

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiang, Ye; Rossmann, Michael G.

2011-12-22

The tailed bacteriophage {phi}29 capsid is decorated with 55 fibers attached to quasi-3-fold symmetry positions. Each fiber is a homotrimer of gene product 8.5 (gp8.5) and consists of two major structural parts, a pseudohexagonal base and a protruding fibrous portion that is about 110 {angstrom} in length. The crystal structure of the C-terminal fibrous portion (residues 112-280) has been determined to a resolution of 1.6 {angstrom}. The structure is about 150 {angstrom} long and shows three distinct structural domains designated as head, neck, and stem. The stem region is a unique three-stranded helix-turn-helix supercoil that has not previously been described.more » When fitted into a cryoelectron microscope reconstruction of the virus, the head structure corresponded to a disconnected density at the distal end of the fiber and the neck structure was located in weak density connecting it to the fiber. Thin section studies of Bacillus subtilis cells infected with fibered or fiberless {phi}29 suggest that the fibers might enhance the attachment of the virions onto the host cell wall.« less

Online Quadrat Study - Site Index

Science.gov Websites

Study Project - Prairie Advocates Project ) Background Information - Data Collection and Entry - Data Data Entry Data Summaries and Graphs Quadrat Study Poster for your classroom. Directions for Looking at by Prairie Study Prairie Experts For Non-Fermilab Prairie researchers: Complete step-by-step

13-Helix folding of a β/γ-peptide manifold designed from a "minimal-constraint" blueprint.

PubMed

Grison, Claire M; Robin, Sylvie; Aitken, David J

2016-06-14

A bottom-up design rationale was adopted to devise β/γ-peptide foldamer manifolds which would adopt preferred 13-helix conformations, relying on minimal steric imposition brought by the constituent amino acid residues. In this way, a well-defined 13-helix conformer was revealed for short oligomers of trans-2-aminocyclobutanecarboxylic acid and γ(4)-amino acids in alternation, which gave good topological superposition upon an α-helix motif.

Soliton compression to few-cycle pulses with a high quality factor by engineering cascaded quadratic nonlinearities.

PubMed

Zeng, Xianglong; Guo, Hairun; Zhou, Binbin; Bache, Morten

2012-11-19

We propose an efficient approach to improve few-cycle soliton compression with cascaded quadratic nonlinearities by using an engineered multi-section structure of the nonlinear crystal. By exploiting engineering of the cascaded quadratic nonlinearities, in each section soliton compression with a low effective order is realized, and high-quality few-cycle pulses with large compression factors are feasible. Each subsequent section is designed so that the compressed pulse exiting the previous section experiences an overall effective self-defocusing cubic nonlinearity corresponding to a modest soliton order, which is kept larger than unity to ensure further compression. This is done by increasing the cascaded quadratic nonlinearity in the new section with an engineered reduced residual phase mismatch. The low soliton orders in each section ensure excellent pulse quality and high efficiency. Numerical results show that compressed pulses with less than three-cycle duration can be achieved even when the compression factor is very large, and in contrast to standard soliton compression, these compressed pulses have minimal pedestal and high quality factor.

Effects of L-glutamate on 1F Helix aspersa neurons

NASA Astrophysics Data System (ADS)

Bernal-Martínez, Juan; Ortega Soto, Arturo

2004-09-01

The aim of this work is to characterize the effect of L-glut and related compounds on the electrical properties of 1F identified neurons of the garden snail Helix aspersa. We used intracellular recording experiments with regular microelectrodes, in current clamp conditions. We report here that the putative L-glut receptor present in 1F Helix neurons has some similarities with the L-glut receptor present in vertebrates, regarding ionic permeability and biophysical properties. However, these responses show different pharmacological properties from those receptors found in vertebrates and mammals.

Reovirus FAST Proteins Drive Pore Formation and Syncytiogenesis Using a Novel Helix-Loop-Helix Fusion-Inducing Lipid Packing Sensor

PubMed Central

Sarker, Muzaddid; de Antueno, Roberto; Langelaan, David N.; Parmar, Hiren B.; Shin, Kyungsoo; Rainey, Jan K.; Duncan, Roy

2015-01-01

Pore formation is the most energy-demanding step during virus-induced membrane fusion, where high curvature of the fusion pore rim increases the spacing between lipid headgroups, exposing the hydrophobic interior of the membrane to water. How protein fusogens breach this thermodynamic barrier to pore formation is unclear. We identified a novel fusion-inducing lipid packing sensor (FLiPS) in the cytosolic endodomain of the baboon reovirus p15 fusion-associated small transmembrane (FAST) protein that is essential for pore formation during cell-cell fusion and syncytiogenesis. NMR spectroscopy and mutational studies indicate the dependence of this FLiPS on a hydrophobic helix-loop-helix structure. Biochemical and biophysical assays reveal the p15 FLiPS preferentially partitions into membranes with high positive curvature, and this partitioning is impeded by bis-ANS, a small molecule that inserts into hydrophobic defects in membranes. Most notably, the p15 FLiPS can be functionally replaced by heterologous amphipathic lipid packing sensors (ALPS) but not by other membrane-interactive amphipathic helices. Furthermore, a previously unrecognized amphipathic helix in the cytosolic domain of the reptilian reovirus p14 FAST protein can functionally replace the p15 FLiPS, and is itself replaceable by a heterologous ALPS motif. Anchored near the cytoplasmic leaflet by the FAST protein transmembrane domain, the FLiPS is perfectly positioned to insert into hydrophobic defects that begin to appear in the highly curved rim of nascent fusion pores, thereby lowering the energy barrier to stable pore formation. PMID:26061049

Quadratic elongation: A quantitative measure of distortion in coordination polyhedra

USGS Publications Warehouse

Robinson, Kelly F.; Gibbs, G.V.; Ribbe, P.H.

1971-01-01

Quadratic elongation and the variance of bond angles are linearly correlated for distorted octahedral and tetrahedral coordination complexes, both of which show variations in bond length and bond angle. The quadratic elonga tion is dimensionless, giving a quantitative measure of polyhedral distortion which is independent of the effective size of the polyhedron.

Folding of a helix is critically stabilized by polarization of backbone hydrogen bonds: study in explicit water.

PubMed

Duan, Li L; Gao, Ya; Mei, Ye; Zhang, Qing G; Tang, Bo; Zhang, John Z H

2012-03-15

Multiple single-trajectory molecular dynamics (MD) simulation at room temperature (300 K) in explicit water was carried out to study the folding dynamics of an α-helix (PDB 2I9M ) using a polarized charge scheme that includes electronic polarization of backbone hydrogen bonds. Starting from an extended conformation, the 17-residue peptide was successfully folded into the native structure (α-helix) between 80 and 130 ns with a root-mean-square deviation of ~1.0 Å. Analysis of the time-dependent trajectories revealed that helix formation of the peptide started at the terminals and progressed toward the center of the peptide. For comparison, MD trajectories generated under various versions of standard AMBER force fields failed to show any significant or stable helix formation in our simulation. Our result shows clear evidence that the electronic polarization of backbone hydrogen bonds energetically stabilizes the helix formation and is critical to the stable folding of the short helix structure. © 2012 American Chemical Society

The positive inside rule is stronger when followed by a transmembrane helix.

PubMed

Virkki, Minttu T; Peters, Christoph; Nilsson, Daniel; Sörensen, Therese; Cristobal, Susana; Wallner, Björn; Elofsson, Arne

2014-08-12

The translocon recognizes transmembrane helices with sufficient level of hydrophobicity and inserts them into the membrane. However, sometimes less hydrophobic helices are also recognized. Positive inside rule, orientational preferences of and specific interactions with neighboring helices have been shown to aid in the recognition of these helices, at least in artificial systems. To better understand how the translocon inserts marginally hydrophobic helices, we studied three naturally occurring marginally hydrophobic helices, which were previously shown to require the subsequent helix for efficient translocon recognition. We find no evidence for specific interactions when we scan all residues in the subsequent helices. Instead, we identify arginines located at the N-terminal part of the subsequent helices that are crucial for the recognition of the marginally hydrophobic transmembrane helices, indicating that the positive inside rule is important. However, in two of the constructs, these arginines do not aid in the recognition without the rest of the subsequent helix; that is, the positive inside rule alone is not sufficient. Instead, the improved recognition of marginally hydrophobic helices can here be explained as follows: the positive inside rule provides an orientational preference of the subsequent helix, which in turn allows the marginally hydrophobic helix to be inserted; that is, the effect of the positive inside rule is stronger if positively charged residues are followed by a transmembrane helix. Such a mechanism obviously cannot aid C-terminal helices, and consequently, we find that the terminal helices in multi-spanning membrane proteins are more hydrophobic than internal helices. Copyright © 2014 Elsevier Ltd. All rights reserved.

Effects of Classroom Instruction on Students' Understanding of Quadratic Equations

ERIC Educational Resources Information Center

Vaiyavutjamai, Pongchawee; Clements, M. A.

2006-01-01

Two hundred and thirty-one students in six Grade 9 classes in two government secondary schools located near Chiang Mai, Thailand, attempted to solve the same 18 quadratic equations before and after participating in 11 lessons on quadratic equations. Data from the students' written responses to the equations, together with data in the form of…

Analyzing Quadratic Unconstrained Binary Optimization Problems Via Multicommodity Flows

PubMed Central

Wang, Di; Kleinberg, Robert D.

2009-01-01

Quadratic Unconstrained Binary Optimization (QUBO) problems concern the minimization of quadratic polynomials in n {0, 1}-valued variables. These problems are NP-complete, but prior work has identified a sequence of polynomial-time computable lower bounds on the minimum value, denoted by C2, C3, C4,…. It is known that C2 can be computed by solving a maximum-flow problem, whereas the only previously known algorithms for computing Ck (k > 2) require solving a linear program. In this paper we prove that C3 can be computed by solving a maximum multicommodity flow problem in a graph constructed from the quadratic function. In addition to providing a lower bound on the minimum value of the quadratic function on {0, 1}n, this multicommodity flow problem also provides some information about the coordinates of the point where this minimum is achieved. By looking at the edges that are never saturated in any maximum multicommodity flow, we can identify relational persistencies: pairs of variables that must have the same or different values in any minimizing assignment. We furthermore show that all of these persistencies can be detected by solving single-commodity flow problems in the same network. PMID:20161596

Analyzing Quadratic Unconstrained Binary Optimization Problems Via Multicommodity Flows.

PubMed

Wang, Di; Kleinberg, Robert D

2009-11-28

Quadratic Unconstrained Binary Optimization (QUBO) problems concern the minimization of quadratic polynomials in n {0, 1}-valued variables. These problems are NP-complete, but prior work has identified a sequence of polynomial-time computable lower bounds on the minimum value, denoted by C(2), C(3), C(4),…. It is known that C(2) can be computed by solving a maximum-flow problem, whereas the only previously known algorithms for computing C(k) (k > 2) require solving a linear program. In this paper we prove that C(3) can be computed by solving a maximum multicommodity flow problem in a graph constructed from the quadratic function. In addition to providing a lower bound on the minimum value of the quadratic function on {0, 1}(n), this multicommodity flow problem also provides some information about the coordinates of the point where this minimum is achieved. By looking at the edges that are never saturated in any maximum multicommodity flow, we can identify relational persistencies: pairs of variables that must have the same or different values in any minimizing assignment. We furthermore show that all of these persistencies can be detected by solving single-commodity flow problems in the same network.

Exploring Quadratic Functions with Logger "Pro"

ERIC Educational Resources Information Center

Pope, Derek

2018-01-01

The author shares the lesson that he used to introduce the quadratic unit to students in an extended second-year algebra class, demonstrate why it was appropriate for his struggling learners, and discuss possible future modifications to this lesson.

Geometrical Solutions of Some Quadratic Equations with Non-Real Roots

ERIC Educational Resources Information Center

Pathak, H. K.; Grewal, A. S.

2002-01-01

This note gives geometrical/graphical methods of finding solutions of the quadratic equation ax[squared] + bx + c = 0, a [not equal to] 0, with non-real roots. Three different cases which give rise to non-real roots of the quadratic equation have been discussed. In case I a geometrical construction and its proof for finding the solutions of the…

Basic helix-loop-helix transcription factors JASMONATE-ASSOCIATED MYC2-LIKE1 (JAM1), JAM2, and JAM3 are negative regulators of jasmonate responses in Arabidopsis.

PubMed

Sasaki-Sekimoto, Yuko; Jikumaru, Yusuke; Obayashi, Takeshi; Saito, Hikaru; Masuda, Shinji; Kamiya, Yuji; Ohta, Hiroyuki; Shirasu, Ken

2013-09-01

Jasmonates regulate transcriptional reprogramming during growth, development, and defense responses. Jasmonoyl-isoleucine, an amino acid conjugate of jasmonic acid (JA), is perceived by the protein complex composed of the F-box protein CORONATINE INSENSITIVE1 (COI1) and JASMONATE ZIM DOMAIN (JAZ) proteins, leading to the ubiquitin-dependent degradation of JAZ proteins. This activates basic helix-loop-helix-type MYC transcription factors to regulate JA-responsive genes. Here, we show that the expression of genes encoding other basic helix-loop-helix transcription factors, JASMONATE ASSOCIATED MYC2-LIKE1 (JAM1), JAM2, and JAM3, is positively regulated in a COI1- and MYC2-dependent manner in Arabidopsis (Arabidopsis thaliana). However, contrary to myc2, the jam1jam2jam3 triple mutant exhibited shorter roots when treated with methyl jasmonate (MJ), indicating enhanced responsiveness to JA. Our genome-wide expression analyses revealed that key jasmonate metabolic genes as well as a set of genes encoding transcription factors that regulate the JA-responsive metabolic genes are negatively regulated by JAMs after MJ treatment. Consistently, loss of JAM genes resulted in higher accumulation of anthocyanin in MJ-treated plants as well as higher accumulation of JA and 12-hydroxyjasmonic acid in wounded plants. These results show that JAMs negatively regulate the JA responses in a manner that is mostly antagonistic to MYC2.

Geometrical and Graphical Solutions of Quadratic Equations.

ERIC Educational Resources Information Center

Hornsby, E. John, Jr.

1990-01-01

Presented are several geometrical and graphical methods of solving quadratic equations. Discussed are Greek origins, Carlyle's method, von Staudt's method, fixed graph methods and imaginary solutions. (CW)

CAD of control systems: Application of nonlinear programming to a linear quadratic formulation

NASA Technical Reports Server (NTRS)

Fleming, P.

1983-01-01

The familiar suboptimal regulator design approach is recast as a constrained optimization problem and incorporated in a Computer Aided Design (CAD) package where both design objective and constraints are quadratic cost functions. This formulation permits the separate consideration of, for example, model following errors, sensitivity measures and control energy as objectives to be minimized or limits to be observed. Efficient techniques for computing the interrelated cost functions and their gradients are utilized in conjunction with a nonlinear programming algorithm. The effectiveness of the approach and the degree of insight into the problem which it affords is illustrated in a helicopter regulation design example.

Highly conserved sequences mediate the dynamic interplay of basic helix-loop-helix proteins regulating retinogenesis.

PubMed

Hernandez, Julio; Matter-Sadzinski, Lidia; Skowronska-Krawczyk, Dorota; Chiodini, Florence; Alliod, Christine; Ballivet, Marc; Matter, Jean-Marc

2007-12-28

The atonal homolog 5 (ATH5) protein is central to the transcriptional network regulating the specification of retinal ganglion cells, and its expression comes under the spatiotemporal control of several basic helix-loop-helix (bHLH) proteins in the course of retina development. Monitoring the in vivo occupancy of the ATH5 promoter by the ATH5, Ngn2, and NeuroM proteins and analyzing the DNA motifs they bind, we show that three evolutionarily conserved E-boxes are required for the bHLH proteins to control the different phases of ATH5 expression. E-box 4 mediates the activity of Ngn2, ATH5, and NeuroM along the pathway leading to the conversion of progenitors into newborn neurons. E-box 1, by mediating the antagonistic effects of Ngn2 and HES1 in proliferating progenitors, controls the expansion of the ATH5 expression domain in early retina. E-box 2 is required for the positive feedback by ATH5 that underlies the up-regulation of ATH5 expression when progenitors are going through their last cell cycle. The combinatorial nature of the regulation of the ATH5 promoter suggests that the bHLH proteins involved have no assigned E-boxes but use a common set at which they either cooperate or compete to finely tune ATH5 expression as development proceeds.

Genome-wide identification and analysis of basic helix-loop-helix domains in dog, Canis lupus familiaris.

PubMed

Wang, Xu-Hua; Wang, Yong; Liu, A-Ke; Liu, Xiao-Ting; Zhou, Yang; Yao, Qin; Chen, Ke-Ping

2015-04-01

The basic helix-loop-helix (bHLH) domain is a highly conserved amino acid motif that defines a group of DNA-binding transcription factors. bHLH proteins play essential regulatory roles in a variety of biological processes in animal, plant, and fungus. The domestic dog, Canis lupus familiaris, is a good model organism for genetic, physiological, and behavioral studies. In this study, we identified 115 putative bHLH genes in the dog genome. Based on a phylogenetic analysis, 51, 26, 14, 4, 12, and 4 dog bHLH genes were assigned to six separate groups (A-F); four bHLH genes were categorized as ''orphans''. Within-group evolutionary relationships inferred from the phylogenetic analysis were consistent with positional conservation, other conserved domains flanking the bHLH motif, and highly conserved intron/exon patterns in other vertebrates. Our analytical results confirmed the GenBank annotations of 89 dog bHLH proteins and provided information that could be used to update the annotations of the remaining 26 dog bHLH proteins. These data will provide good references for further studies on the structures and regulatory functions of bHLH proteins in the growth and development of dogs, which may help in understanding the mechanisms that underlie the physical and behavioral differences between dogs and wolves.

DNA binding specificity of the basic-helix-loop-helix protein MASH-1.

PubMed

Meierhan, D; el-Ariss, C; Neuenschwander, M; Sieber, M; Stackhouse, J F; Allemann, R K

1995-09-05

Despite the high degree of sequence similarity in their basic-helix-loop-helix (BHLH) domains, MASH-1 and MyoD are involved in different biological processes. In order to define possible differences between the DNA binding specificities of these two proteins, we investigated the DNA binding properties of MASH-1 by circular dichroism spectroscopy and by electrophoretic mobility shift assays (EMSA). Upon binding to DNA, the BHLH domain of MASH-1 underwent a conformational change from a mainly unfolded to a largely alpha-helical form, and surprisingly, this change was independent of the specific DNA sequence. The same conformational transition could be induced by the addition of 20% 2,2,2-trifluoroethanol. The apparent dissociation constants (KD) of the complexes of full-length MASH-1 with various oligonucleotides were determined from half-saturation points in EMSAs. MASH-1 bound as a dimer to DNA sequences containing an E-box with high affinity KD = 1.4-4.1 x 10(-14) M2). However, the specificity of DNA binding was low. The dissociation constant for the complex between MASH-1 and the highest affinity E-box sequence (KD = 1.4 x 10(-14) M2) was only a factor of 10 smaller than for completely unrelated DNA sequences (KD = approximately 1 x 10(-13) M2). The DNA binding specificity of MASH-1 was not significantly increased by the formation of an heterodimer with the ubiquitous E12 protein. MASH-1 and MyoD displayed similar binding site preferences, suggesting that their different target gene specificities cannot be explained solely by differential DNA binding. An explanation for these findings is provided on the basis of the known crystal structure of the BHLH domain of MyoD.

The Recombinant Inhibitor of DNA Binding Id2 Forms Multimeric Structures via the Helix-Loop-Helix Domain and the Nuclear Export Signal.

PubMed

Roschger, Cornelia; Schubert, Mario; Regl, Christof; Andosch, Ancuela; Marquez, Augusto; Berger, Thomas; Huber, Christian G; Lütz-Meindl, Ursula; Cabrele, Chiara

2018-04-07

The inhibitor of DNA binding and cell differentiation 2 (Id2) is a helix-loop-helix (HLH) protein that acts as negative dominant regulator of basic-HLH transcription factors during development and in cancer. The structural properties of Id2 have been investigated so far by using synthetic or recombinant fragments reproducing single domains (N-terminus, HLH, C-terminus): the HLH domain tends to dimerize into a four-helix bundle, whereas the flanking regions are flexible. In this work, the intact protein was expressed in E. coli , solubilized from inclusion bodies with urea, purified and dissolved in water at pH~4. Under these conditions, Id2 was obtained with both cysteine residues disulfide-bonded to β-mercaptoethanol that was present during the solubilization process. Moreover, it existed in a self-assembled state, in which the N-terminus remained highly flexible, while the HLH domain and, surprisingly, part of the C-terminus, which corresponds to the nuclear export signal (NES), both were involved in slowly tumbling, rigid structures. The protein oligomers also formed twisted fibrils that were several micrometers long and up to 80 nm thick. These results show that self-assembly decreases the backbone flexibility of those two protein regions (HLH and NES) that are important for interaction with basic-HLH transcription factors or for nucleocytoplasmic shuttling.

The SUMO Pathway Promotes Basic Helix-Loop-Helix Proneural Factor Activity via a Direct Effect on the Zn Finger Protein Senseless

PubMed Central

Chen, Angela; Huang, Yan Chang; Wang, Pin Yao; Kemp, Sadie E.

2012-01-01

During development, proneural transcription factors of the basic helix-loop-helix (bHLH) family are required to commit cells to a neural fate. In Drosophila neurogenesis, a key mechanism promoting sense organ precursor (SOP) fate is the synergy between proneural factors and their coactivator Senseless in transcriptional activation of target genes. Here we present evidence that posttranslational modification by SUMO enhances this synergy via an effect on Senseless protein. We show that Senseless is a direct target for SUMO modification and that mutagenesis of a predicted SUMOylation motif in Senseless reduces Senseless/proneural synergy both in vivo and in cell culture. We propose that SUMOylation of Senseless via lysine 509 promotes its synergy with proneural proteins during transcriptional activation and hence regulates an important step in neurogenesis leading to the formation and maturation of the SOPs. PMID:22586269

Quadratic spatial soliton interactions

NASA Astrophysics Data System (ADS)

Jankovic, Ladislav

Quadratic spatial soliton interactions were investigated in this Dissertation. The first part deals with characterizing the principal features of multi-soliton generation and soliton self-reflection. The second deals with two beam processes leading to soliton interactions and collisions. These subjects were investigated both theoretically and experimentally. The experiments were performed by using potassium niobate (KNBO 3) and periodically poled potassium titanyl phosphate (KTP) crystals. These particular crystals were desirable for these experiments because of their large nonlinear coefficients and, more importantly, because the experiments could be performed under non-critical-phase-matching (NCPM) conditions. The single soliton generation measurements, performed on KNBO3 by launching the fundamental component only, showed a broad angular acceptance bandwidth which was important for the soliton collisions performed later. Furthermore, at high input intensities multi-soliton generation was observed for the first time. The influence on the multi-soliton patterns generated of the input intensity and beam symmetry was investigated. The combined experimental and theoretical efforts indicated that spatial and temporal noise on the input laser beam induced multi-soliton patterns. Another research direction pursued was intensity dependent soliton routing by using of a specially engineered quadratically nonlinear interface within a periodically poled KTP sample. This was the first time demonstration of the self-reflection phenomenon in a system with a quadratic nonlinearity. The feature investigated is believed to have a great potential for soliton routing and manipulation by engineered structures. A detailed investigation was conducted on two soliton interaction and collision processes. Birth of an additional soliton resulting from a two soliton collision was observed and characterized for the special case of a non-planar geometry. A small amount of spiraling, up to 30

Fluorophores, environments, and quantification techniques in the analysis of transmembrane helix interaction using FRET.

PubMed

Khadria, Ambalika S; Senes, Alessandro

2015-07-01

Förster resonance energy transfer (FRET) has been widely used as a spectroscopic tool in vitro to study the interactions between transmembrane (TM) helices in detergent and lipid environments. This technique has been instrumental to many studies that have greatly contributed to quantitative understanding of the physical principles that govern helix-helix interactions in the membrane. These studies have also improved our understanding of the biological role of oligomerization in membrane proteins. In this review, we focus on the combinations of fluorophores used, the membrane mimetic environments, and measurement techniques that have been applied to study model systems as well as biological oligomeric complexes in vitro. We highlight the different formalisms used to calculate FRET efficiency and the challenges associated with accurate quantification. The goal is to provide the reader with a comparative summary of the relevant literature for planning and designing FRET experiments aimed at measuring TM helix-helix associations. © 2015 Wiley Periodicals, Inc.

The Bridge Helix of RNA polymerase acts as a central nanomechanical switchboard for coordinating catalysis and substrate movement.

PubMed

Weinzierl, Robert O J

2011-01-01

The availability of in vitro assembly systems to produce recombinant archaeal RNA polymerases (RNAPs) offers one of the most powerful experimental tools for investigating the still relatively poorly understood molecular mechanisms underlying RNAP function. Over the last few years, we pioneered new robot-based high-throughput mutagenesis approaches to study structure/function relationships within various domains surrounding the catalytic center. The Bridge Helix domain, which appears in numerous X-ray structures as a 35-amino-acid-long alpha helix, coordinates the concerted movement of several other domains during catalysis through kinking of two discrete molecular hinges. Mutations affecting these kinking mechanisms have a direct effect on the specific catalytic activity of RNAP and can in some instances more than double it. Molecular dynamics simulations have established themselves as exceptionally useful for providing additional insights and detailed models to explain the underlying structural motions.

The secondary structure of the ets domain of human Fli-1 resembles that of the helix-turn-helix DNA-binding motif of the Escherichia coli catabolite gene activator protein.

PubMed Central

Liang, H; Olejniczak, E T; Mao, X; Nettesheim, D G; Yu, L; Thompson, C B; Fesik, S W

1994-01-01

The ets family of eukaryotic transcription factors is characterized by a conserved DNA-binding domain of approximately 85 amino acids for which the three-dimensional structure is not known. By using multidimensional NMR spectroscopy, we have determined the secondary structure of the ets domain of one member of this gene family, human Fli-1, both in the free form and in a complex with a 16-bp cognate DNA site. The secondary structure of the Fli-1 ets domain consists of three alpha-helices and a short four-stranded antiparallel beta-sheet. This secondary structure arrangement resembles that of the DNA-binding domain of the catabolite gene activator protein of Escherichia coli, as well as those of several eukaryotic DNA-binding proteins including histone H5, HNF-3/fork head, and the heat shock transcription factor. Differences in chemical shifts of backbone resonances and amide exchange rates between the DNA-bound and free forms of the Fli-1 ets domain suggest that the third helix is the DNA recognition helix, as in the catabolite gene activator protein and other structurally related proteins. These results suggest that the ets domain is structurally similar to the catabolite gene activator protein family of helix-turn-helix DNA-binding proteins. Images PMID:7972119

Effective scoring of scapha prevents helix irregularity in prominent ear correction - a biomechanical study.

PubMed

Nagasao, Tomohisa; Miyamoto, Junpei; Shimizu, Yusuke; Kasai, Shogo; Kishi, Kazuo; Kaneko, Tsuyoshi

2014-09-01

As the antihelix is created in the operation for prominent ear, the helix often presents irregularities. This biomechanical study aims to elucidate effective techniques to prevent these irregularities. Finite element models were produced simulating 10 prominent ears. The scaphas of the 10 models were thinned to simulate scoring or abrasion of the cartilage. The thinning was conducted in four fashions. In the first group, no thinning was conducted (Non-Scoring Models); in the second group, the upper half of the scapha was thinned (Upper-Scoring Models); in the third group, the lower half of the scapha was thinned (Lower-Scoring Models); in the fourth group, the whole scapha was thinned (Whole-Scoring Models). Mattress sutures were applied to create the antihelix to simulate Mustarde's in-suture technique. Thereafter, transformation of the helix's contour was evaluated. Irregularity developed on the upper region of the helix with Non-Scoring and Lower-Scoring Models; the degree of the upper-region's irregularity was reduced with Upper-Scoring Models and Whole-Scoring Models. Although the edge of the helix moved in the posterior-medial direction with other type models, it moved in the anterior direction with Whole-Scoring Models. Irregularity of the upper region of the helix can be prevented by performing scoring or abrasion of the upper part of the scapha. The prominence of the helix and width of the auricle are adjustable by varying the areas of the scapha receiving scoring or abrasion. These findings are useful in improving operative outcomes in the treatment of prominent ears. Copyright © 2014 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Finite Element Simulation of Articular Contact Mechanics with Quadratic Tetrahedral Elements

PubMed Central

Maas, Steve A.; Ellis, Benjamin J.; Rawlins, David S.; Weiss, Jeffrey A.

2016-01-01

Although it is easier to generate finite element discretizations with tetrahedral elements, trilinear hexahedral (HEX8) elements are more often used in simulations of articular contact mechanics. This is due to numerical shortcomings of linear tetrahedral (TET4) elements, limited availability of quadratic tetrahedron elements in combination with effective contact algorithms, and the perceived increased computational expense of quadratic finite elements. In this study we implemented both ten-node (TET10) and fifteen-node (TET15) quadratic tetrahedral elements in FEBio (www.febio.org) and compared their accuracy, robustness in terms of convergence behavior and computational cost for simulations relevant to articular contact mechanics. Suitable volume integration and surface integration rules were determined by comparing the results of several benchmark contact problems. The results demonstrated that the surface integration rule used to evaluate the contact integrals for quadratic elements affected both convergence behavior and accuracy of predicted stresses. The computational expense and robustness of both quadratic tetrahedral formulations compared favorably to the HEX8 models. Of note, the TET15 element demonstrated superior convergence behavior and lower computational cost than both the TET10 and HEX8 elements for meshes with similar numbers of degrees of freedom in the contact problems that we examined. Finally, the excellent accuracy and relative efficiency of these quadratic tetrahedral elements was illustrated by comparing their predictions with those for a HEX8 mesh for simulation of articular contact in a fully validated model of the hip. These results demonstrate that TET10 and TET15 elements provide viable alternatives to HEX8 elements for simulation of articular contact mechanics. PMID:26900037

Finite element simulation of articular contact mechanics with quadratic tetrahedral elements.

PubMed

Maas, Steve A; Ellis, Benjamin J; Rawlins, David S; Weiss, Jeffrey A

2016-03-21

Although it is easier to generate finite element discretizations with tetrahedral elements, trilinear hexahedral (HEX8) elements are more often used in simulations of articular contact mechanics. This is due to numerical shortcomings of linear tetrahedral (TET4) elements, limited availability of quadratic tetrahedron elements in combination with effective contact algorithms, and the perceived increased computational expense of quadratic finite elements. In this study we implemented both ten-node (TET10) and fifteen-node (TET15) quadratic tetrahedral elements in FEBio (www.febio.org) and compared their accuracy, robustness in terms of convergence behavior and computational cost for simulations relevant to articular contact mechanics. Suitable volume integration and surface integration rules were determined by comparing the results of several benchmark contact problems. The results demonstrated that the surface integration rule used to evaluate the contact integrals for quadratic elements affected both convergence behavior and accuracy of predicted stresses. The computational expense and robustness of both quadratic tetrahedral formulations compared favorably to the HEX8 models. Of note, the TET15 element demonstrated superior convergence behavior and lower computational cost than both the TET10 and HEX8 elements for meshes with similar numbers of degrees of freedom in the contact problems that we examined. Finally, the excellent accuracy and relative efficiency of these quadratic tetrahedral elements was illustrated by comparing their predictions with those for a HEX8 mesh for simulation of articular contact in a fully validated model of the hip. These results demonstrate that TET10 and TET15 elements provide viable alternatives to HEX8 elements for simulation of articular contact mechanics. Copyright © 2016 Elsevier Ltd. All rights reserved.

On Volterra quadratic stochastic operators with continual state space

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ganikhodjaev, Nasir; Hamzah, Nur Zatul Akmar

2015-05-15

Let (X,F) be a measurable space, and S(X,F) be the set of all probability measures on (X,F) where X is a state space and F is σ - algebraon X. We consider a nonlinear transformation (quadratic stochastic operator) defined by (Vλ)(A) = ∫{sub X}∫{sub X}P(x,y,A)dλ(x)dλ(y), where P(x, y, A) is regarded as a function of two variables x and y with fixed A ∈ F . A quadratic stochastic operator V is called a regular, if for any initial measure the strong limit lim{sub n→∞} V{sup n }(λ) is exists. In this paper, we construct a family of quadratic stochastic operators defined on themore » segment X = [0,1] with Borel σ - algebra F on X , prove their regularity and show that the limit measure is a Dirac measure.« less

Schur Stability Regions for Complex Quadratic Polynomials

ERIC Educational Resources Information Center

Cheng, Sui Sun; Huang, Shao Yuan

2010-01-01

Given a quadratic polynomial with complex coefficients, necessary and sufficient conditions are found in terms of the coefficients such that all its roots have absolute values less than 1. (Contains 3 figures.)

Helix - Phases 1 and 2

DTIC Science & Technology

2013-12-20

20 Helix    –  Phases  1  and  2   Technical  Report  SERC-­‐2013-­‐TR-­‐038-­‐2   December  20,  2013     Research  Team...under   Research  Topics  45  and  106               Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the...WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Stevens Institute of Technology,Systems Engineering Research Center,Castle Point

Linear and quadratic static response functions and structure functions in Yukawa liquids.

PubMed

Magyar, Péter; Donkó, Zoltán; Kalman, Gabor J; Golden, Kenneth I

2014-08-01

We compute linear and quadratic static density response functions of three-dimensional Yukawa liquids by applying an external perturbation potential in molecular dynamics simulations. The response functions are also obtained from the equilibrium fluctuations (static structure factors) in the system via the fluctuation-dissipation theorems. The good agreement of the quadratic response functions, obtained in the two different ways, confirms the quadratic fluctuation-dissipation theorem. We also find that the three-point structure function may be factorizable into two-point structure functions, leading to a cluster representation of the equilibrium triplet correlation function.

Identification and expression analysis of the apple (Malus × domestica) basic helix-loop-helix transcription factor family.

PubMed

Yang, Jinhua; Gao, Min; Huang, Li; Wang, Yaqiong; van Nocker, Steve; Wan, Ran; Guo, Chunlei; Wang, Xiping; Gao, Hua

2017-02-09

Basic helix-loop-helix (bHLH) proteins, which are characterized by a conserved bHLH domain, comprise one of the largest families of transcription factors in both plants and animals, and have been shown to have a wide range of biological functions. However, there have been very few studies of bHLH proteins from perennial tree species. We describe here the identification and characterization of 175 bHLH transcription factors from apple (Malus × domestica). Phylogenetic analysis of apple bHLH (MdbHLH) genes and their Arabidopsis thaliana (Arabidopsis) orthologs indicated that they can be classified into 23 subgroups. Moreover, integrated synteny analysis suggested that the large-scale expansion of the bHLH transcription factor family occurred before the divergence of apple and Arabidopsis. An analysis of the exon/intron structure and protein domains was conducted to suggest their functional roles. Finally, we observed that MdbHLH subgroup III and IV genes displayed diverse expression profiles in various organs, as well as in response to abiotic stresses and various hormone treatments. Taken together, these data provide new information regarding the composition and diversity of the apple bHLH transcription factor family that will provide a platform for future targeted functional characterization.

Assessment of vertical changes during maxillary expansion using quad helix or bonded rapid maxillary expander.

PubMed

Conroy-Piskai, Cara; Galang-Boquiren, Maria Therese S; Obrez, Ales; Viana, Maria Grace Costa; Oppermann, Nelson; Sanchez, Flavio; Edgren, Bradford; Kusnoto, Budi

2016-11-01

To determine if there is a significantly different effect on vertical changes during phase I palatal expansion treatment using a quad helix and a bonded rapid maxillary expander in growing skeletal Class I and Class II patients. This retrospective study looked at 2 treatment groups, a quad helix group and a bonded rapid maxillary expander group, before treatment (T1) and at the completion of phase I treatment (T2). Each treatment group was compared to an untreated predicted growth model. Lateral cephalograms at T1 and T2 were traced and analyzed for changes in vertical dimension. No differences were found between the treatment groups at T1, but significant differences at T2 were found for convexity, lower facial height, total facial height, facial axis, and Frankfort Mandibular Plane Angle (FMA) variables. A comparison of treatment groups at T2 to their respective untreated predicted growth models found a significant difference for the lower facial height variable in the quad helix group and for the upper first molar to palatal plane (U6-PP) variable in the bonded expander group. Overall, both the quad helix expander and the bonded rapid maxillary expander showed minimal vertical changes during palatal expansion treatment. The differences at T2 suggested that the quad helix expander had more control over skeletal vertical measurements. When comparing treatment results to untreated predicted growth values, the quad helix expander appeared to better maintain lower facial height and the bonded rapid maxillary expander appeared to better maintain the maxillary first molar vertical height.

Geometrical Solutions of Quadratic Equations.

ERIC Educational Resources Information Center

Grewal, A. S.; Godloza, L.

1999-01-01

Demonstrates that the equation of a circle (x-h)2 + (y-k)2 = r2 with center (h; k) and radius r reduces to a quadratic equation x2-2xh + (h2 + k2 -r2) = O at the intersection with the x-axis. Illustrates how to determine the center of a circle as well as a point on a circle. (Author/ASK)

A modular synthesis of teraryl-based α-helix mimetics, part 1: Synthesis of core fragments with two electronically differentiated leaving groups.

PubMed

Peters, Martin; Trobe, Melanie; Tan, Hao; Kleineweischede, Rolf; Breinbauer, Rolf

2013-02-11

Teraryl-based α-helix mimetics have proven to be useful compounds for the inhibition of protein-protein interactions (PPI). We have developed a modular and flexible approach for the synthesis of teraryl-based α-helix mimetics. Central to our strategy is the use of a benzene core unit featuring two leaving groups of differentiated reactivity in the Pd-catalyzed cross-coupling used for terphenyl assembly. With the halogen/diazonium route and the halogen/triflate route, two strategies have successfully been established. The synthesis of core building blocks with aliphatic (Ala, Val, Leu, Ile), aromatic (Phe), polar (Cys, Lys), hydrophilic (Ser, Gln), and acidic (Glu) amino acid side chains are reported. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The energetic basis of the DNA double helix: a combined microcalorimetric approach

PubMed Central

Vaitiekunas, Paulius; Crane-Robinson, Colyn; Privalov, Peter L.

2015-01-01

Microcalorimetric studies of DNA duplexes and their component single strands showed that association enthalpies of unfolded complementary strands into completely folded duplexes increase linearly with temperature and do not depend on salt concentration, i.e. duplex formation results in a constant heat capacity decrement, identical for CG and AT pairs. Although duplex thermostability increases with CG content, the enthalpic and entropic contributions of an AT pair to duplex formation exceed that of a CG pair when compared at the same temperature. The reduced contribution of AT pairs to duplex stabilization comes not from their lower enthalpy, as previously supposed, but from their larger entropy contribution. This larger enthalpy and particularly the greater entropy results from water fixed by the AT pair in the minor groove. As the increased entropy of an AT pair exceeds that of melting ice, the water molecule fixed by this pair must affect those of its neighbors. Water in the minor groove is, thus, orchestrated by the arrangement of AT groups, i.e. is context dependent. In contrast, water hydrating exposed nonpolar surfaces of bases is responsible for the heat capacity increment on dissociation and, therefore, for the temperature dependence of all thermodynamic characteristics of the double helix. PMID:26304541

"helix Nebula - the Science Cloud", a European Science Driven Cross-Domain Initiative Implemented in via AN Active Ppp Set-Up

NASA Astrophysics Data System (ADS)

Lengert, W.; Mondon, E.; Bégin, M. E.; Ferrer, M.; Vallois, F.; DelaMar, J.

2015-12-01

Helix Nebula, a European science cross-domain initiative building on an active PPP, is aiming to implement the concept of an open science commons[1] while using a cloud hybrid model[2] as the proposed implementation solution. This approach allows leveraging and merging of complementary data intensive Earth Science disciplines (e.g. instrumentation[3] and modeling), without introducing significant changes in the contributors' operational set-up. Considering the seamless integration with life-science (e.g. EMBL), scientific exploitation of meteorological, climate, and Earth Observation data and models open an enormous potential for new big data science. The work of Helix Nebula has shown that is it feasible to interoperate publicly funded infrastructures, such as EGI [5] and GEANT [6], with commercial cloud services. Such hybrid systems are in the interest of the existing users of publicly funded infrastructures and funding agencies because they will provide "freedom and choice" over the type of computing resources to be consumed and the manner in which they can be obtained. But to offer such freedom and choice across a spectrum of suppliers, various issues such as intellectual property, legal responsibility, service quality agreements and related issues need to be addressed. Finding solutions to these issues is one of the goals of the Helix Nebula initiative. [1] http://www.egi.eu/news-and-media/publications/OpenScienceCommons_v3.pdf [2] http://www.helix-nebula.eu/events/towards-the-european-open-science-cloud [3] e.g. https://sentinel.esa.int/web/sentinel/sentinel-data-access [5] http://www.egi.eu/ [6] http://www.geant.net/

Quadratic String Method for Locating Instantons in Tunneling Splitting Calculations.

PubMed

Cvitaš, Marko T

2018-03-13

The ring-polymer instanton (RPI) method is an efficient technique for calculating approximate tunneling splittings in high-dimensional molecular systems. In the RPI method, tunneling splitting is evaluated from the properties of the minimum action path (MAP) connecting the symmetric wells, whereby the extensive sampling of the full potential energy surface of the exact quantum-dynamics methods is avoided. Nevertheless, the search for the MAP is usually the most time-consuming step in the standard numerical procedures. Recently, nudged elastic band (NEB) and string methods, originaly developed for locating minimum energy paths (MEPs), were adapted for the purpose of MAP finding with great efficiency gains [ J. Chem. Theory Comput. 2016 , 12 , 787 ]. In this work, we develop a new quadratic string method for locating instantons. The Euclidean action is minimized by propagating the initial guess (a path connecting two wells) over the quadratic potential energy surface approximated by means of updated Hessians. This allows the algorithm to take many minimization steps between the potential/gradient calls with further reductions in the computational effort, exploiting the smoothness of potential energy surface. The approach is general, as it uses Cartesian coordinates, and widely applicable, with computational effort of finding the instanton usually lower than that of determining the MEP. It can be combined with expensive potential energy surfaces or on-the-fly electronic-structure methods to explore a wide variety of molecular systems.

The non-avian theropod quadrate I: standardized terminology with an overview of the anatomy and function

PubMed Central

Araújo, Ricardo; Mateus, Octávio

2015-01-01

The quadrate of reptiles and most other tetrapods plays an important morphofunctional role by allowing the articulation of the mandible with the cranium. In Theropoda, the morphology of the quadrate is particularly complex and varies importantly among different clades of non-avian theropods, therefore conferring a strong taxonomic potential. Inconsistencies in the notation and terminology used in discussions of the theropod quadrate anatomy have been noticed, including at least one instance when no less than eight different terms were given to the same structure. A standardized list of terms and notations for each quadrate anatomical entity is proposed here, with the goal of facilitating future descriptions of this important cranial bone. In addition, an overview of the literature on quadrate function and pneumaticity in non-avian theropods is presented, along with a discussion of the inferences that could be made from this research. Specifically, the quadrate of the large majority of non-avian theropods is akinetic but the diagonally oriented intercondylar sulcus of the mandibular articulation allowed both rami of the mandible to move laterally when opening the mouth in many of theropods. Pneumaticity of the quadrate is also present in most averostran clades and the pneumatic chamber—invaded by the quadrate diverticulum of the mandibular arch pneumatic system—was connected to one or several pneumatic foramina on the medial, lateral, posterior, anterior or ventral sides of the quadrate. PMID:26401455

The basic helix-loop-helix region of the transcriptional repressor hairy and enhancer of split 1 is preorganized to bind DNA.

PubMed

Popovic, Matija; Wienk, Hans; Coglievina, Maristella; Boelens, Rolf; Pongor, Sándor; Pintar, Alessandro

2014-04-01

Hairy and enhancer of split 1, one of the main downstream effectors in Notch signaling, is a transcriptional repressor of the basic helix-loop-helix (bHLH) family. Using nuclear magnetic resonance methods, we have determined the structure and dynamics of a recombinant protein, H1H, which includes an N-terminal segment, b1, containing functionally important phosphorylation sites, the basic region b2, required for binding to DNA, and the HLH domain. We show that a proline residue in the sequence divides the protein in two parts, a flexible and disordered N-terminal region including b1 and a structured, mainly helical region comprising b2 and the HLH domain. Binding of H1H to a double strand DNA oligonucleotide was monitored through the chemical shift perturbation of backbone amide resonances, and showed that the interaction surface involves not only the b2 segment but also several residues in the b1 and HLH regions. Copyright © 2014 Wiley Periodicals, Inc.

Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix

PubMed Central

Brown, Jessica A.; Bulkley, David; Wang, Jimin; Valenstein, Max L.; Yario, Therese A.; Steitz, Thomas A.; Steitz, Joan A.

2014-01-01

Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a highly-abundant nuclear long noncoding RNA that promotes malignancy. A 3′-stem-loop structure is predicted to confer stability by engaging a downstream A-rich tract in a triple helix, similar to the expression and nuclear retention element (ENE) from the KSHV polyadenylated nuclear RNA. The 3.1-Å resolution crystal structure of the human MALAT1 ENE and A-rich tract reveals a bipartite triple helix containing stacks of five and four U•A-U triples separated by a C+•G-C triplet and C-G doublet, extended by two A-minor interactions. In vivo decay assays indicate that this blunt-ended triple helix, with the 3′ nucleotide in a U•A-U triple, inhibits rapid nuclear RNA decay. Interruption of the triple helix by the C-G doublet induces a “helical reset” that explains why triple-helical stacks longer than six do not occur in nature. PMID:24952594

Constitutive Overexpression of the Basic Helix-Loop-Helix Nex1/MATH-2 Transcription Factor Promotes Neuronal Differentiation of PC12 Cells and Neurite Regeneration

PubMed Central

Uittenbogaard, Martine; Chiaramello, Anne

2009-01-01

Elucidation of the intricate transcriptional pathways leading to neural differentiation and the establishment of neuronal identity is critical to the understanding and design of therapeutic approaches. Among the important players, the basic helix-loop-helix (bHLH) transcription factors have been found to be pivotal regulators of neurogenesis. In this study, we investigate the role of the bHLH differentiation factor Nex1/MATH-2 in conjunction with the nerve growth factor (NGF) signaling pathway using the rat phenochromocytoma PC12 cell line. We report that the expression of Nex1 protein is induced after 5 hr of NGF treatment and reaches maximal levels at 24 hr, when very few PC12 cells have begun extending neurites and ceased cell division. Furthermore, our study demonstrates that Nex1 has the ability to trigger neuronal differentiation of PC12 cells in the absence of neurotrophic factor. We show that Nex1 plays an important role in neurite outgrowth and has the capacity to regenerate neurite outgrowth in the absence of NGF. These results are corroborated by the fact that Nex1 targets a repertoire of distinct types of genes associated with neuronal differentiation, such as GAP-43, βIII-tubulin, and NeuroD. In addition, our findings show that Nex1 up-regulates the expression of the mitotic inhibitor p21WAF1, thus linking neuronal differentiation to cell cycle withdrawal. Finally, our studies show that overexpression of a Nex1 mutant has the ability to block the execution of NGF-induced differentiation program, suggesting that Nex1 may be an important effector of the NGF signaling pathway. PMID:11782967

Effect of sterically demanding substituents on the conformational stability of the collagen triple helix.

PubMed

Erdmann, Roman S; Wennemers, Helma

2012-10-17

The effect of sterically demanding groups at proline residues on the conformational stability of the collagen triple helix was examined. The thermal stabilities (T(m) and ΔG) of eight different triple helices derived from collagen model peptides with (4R)- or (4S)-configured amidoprolines bearing either methyl or bulkier tert-butyl groups in the Xaa or Yaa position were determined and served as a relative measure for the conformational stability of the corresponding collagen triple helices. The results show that sterically demanding substituents are tolerated in the collagen triple helix when they are attached to (4R)-configured amidoprolines in the Xaa position or to (4S)-configured amidoprolines in the Yaa position. Structural studies in which the preferred conformation of (4R)- or (4S)-configured amidoproline were overlaid with the Pro and Hyp residues within a crystal structure of collagen revealed that the sterically demanding groups point to the outside of these two triple helices and thereby do not interfere with the formation of the triple helix. In all of the other examined collagen derivatives with lower stability of the triple helices, the acetyl or pivaloyl residues point toward the inside of the triple helix and clash with a residue of the neighboring strand. The results also revealed that unfavorable steric dispositions affect the conformational stability of the collagen triple helix more than unfavorable ring puckers of the proline residues. The results are useful for the design of functionalized collagen based materials.

A Wavelet Bicoherence-Based Quadratic Nonlinearity Feature for Translational Axis Condition Monitoring

PubMed Central

Li, Yong; Wang, Xiufeng; Lin, Jing; Shi, Shengyu

2014-01-01

The translational axis is one of the most important subsystems in modern machine tools, as its degradation may result in the loss of the product qualification and lower the control precision. Condition-based maintenance (CBM) has been considered as one of the advanced maintenance schemes to achieve effective, reliable and cost-effective operation of machine systems, however, current vibration-based maintenance schemes cannot be employed directly in the translational axis system, due to its complex structure and the inefficiency of commonly used condition monitoring features. In this paper, a wavelet bicoherence-based quadratic nonlinearity feature is proposed for translational axis condition monitoring by using the torque signature of the drive servomotor. Firstly, the quadratic nonlinearity of the servomotor torque signature is discussed, and then, a biphase randomization wavelet bicoherence is introduced for its quadratic nonlinear detection. On this basis, a quadratic nonlinearity feature is proposed for condition monitoring of the translational axis. The properties of the proposed quadratic nonlinearity feature are investigated by simulations. Subsequently, this feature is applied to the real-world servomotor torque data collected from the X-axis on a high precision vertical machining centre. All the results show that the performance of the proposed feature is much better than that of original condition monitoring features. PMID:24473281

De novo design, synthesis and characterisation of MP3, a new catalytic four-helix bundle hemeprotein.

PubMed

Faiella, Marina; Maglio, Ornella; Nastri, Flavia; Lombardi, Angela; Lista, Liliana; Hagen, Wilfred R; Pavone, Vincenzo

2012-12-07

A new artificial metalloenzyme, MP3 (MiniPeroxidase 3), designed by combining the excellent structural properties of four-helix bundle protein scaffolds with the activity of natural peroxidases, was synthesised and characterised. This new hemeprotein model was developed by covalently linking the deuteroporphyrin to two peptide chains of different compositions to obtain an asymmetric helix-loop-helix/heme/helix-loop-helix sandwich arrangement, characterised by 1) a His residue on one chain that acts as an axial ligand to the iron ion; 2) a vacant distal site that is able to accommodate exogenous ligands or substrates; and 3) an Arg residue in the distal site that should assist in hydrogen peroxide activation to give an HRP-like catalytic process. MP3 was synthesised and characterised as its iron complex. CD measurements revealed the high helix-forming propensity of the peptide, confirming the appropriateness of the model procedure; UV/Vis, MCD and EPR experiments gave insights into the coordination geometry and the spin state of the metal. Kinetic experiments showed that Fe(III)-MP3 possesses peroxidase-like activity comparable to R38A-hHRP, highlighting the possibility of mimicking the functional features of natural enzymes. The synergistic application of de novo design methods, synthetic procedures, and spectroscopic characterisation, described herein, demonstrates a method by which to implement and optimise catalytic activity for an enzyme mimetic. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quadratic canonical transformation theory and higher order density matrices.

PubMed

Neuscamman, Eric; Yanai, Takeshi; Chan, Garnet Kin-Lic

2009-03-28

Canonical transformation (CT) theory provides a rigorously size-extensive description of dynamic correlation in multireference systems, with an accuracy superior to and cost scaling lower than complete active space second order perturbation theory. Here we expand our previous theory by investigating (i) a commutator approximation that is applied at quadratic, as opposed to linear, order in the effective Hamiltonian, and (ii) incorporation of the three-body reduced density matrix in the operator and density matrix decompositions. The quadratic commutator approximation improves CT's accuracy when used with a single-determinant reference, repairing the previous formal disadvantage of the single-reference linear CT theory relative to singles and doubles coupled cluster theory. Calculations on the BH and HF binding curves confirm this improvement. In multireference systems, the three-body reduced density matrix increases the overall accuracy of the CT theory. Tests on the H(2)O and N(2) binding curves yield results highly competitive with expensive state-of-the-art multireference methods, such as the multireference Davidson-corrected configuration interaction (MRCI+Q), averaged coupled pair functional, and averaged quadratic coupled cluster theories.

Triple Helix Systems: An Analytical Framework for Innovation Policy and Practice in the Knowledge Society

ERIC Educational Resources Information Center

Ranga, Marina; Etzkowitz, Henry

2013-01-01

This paper introduces the concept of Triple Helix systems as an analytical construct that synthesizes the key features of university--industry--government (Triple Helix) interactions into an "innovation system" format, defined according to systems theory as a set of components, relationships and functions. Among the components of Triple…

Differences between quadratic equations and functions: Indonesian pre-service secondary mathematics teachers’ views

NASA Astrophysics Data System (ADS)

Aziz, T. A.; Pramudiani, P.; Purnomo, Y. W.

2018-01-01

Difference between quadratic equation and quadratic function as perceived by Indonesian pre-service secondary mathematics teachers (N = 55) who enrolled at one private university in Jakarta City was investigated. Analysis of participants’ written responses and interviews were conducted consecutively. Participants’ written responses highlighted differences between quadratic equation and function by referring to their general terms, main characteristics, processes, and geometrical aspects. However, they showed several obstacles in describing the differences such as inappropriate constraints and improper interpretations. Implications of the study are discussed.

An Improved Correction for Range Restricted Correlations Under Extreme, Monotonic Quadratic Nonlinearity and Heteroscedasticity.

PubMed

Culpepper, Steven Andrew

2016-06-01

Standardized tests are frequently used for selection decisions, and the validation of test scores remains an important area of research. This paper builds upon prior literature about the effect of nonlinearity and heteroscedasticity on the accuracy of standard formulas for correcting correlations in restricted samples. Existing formulas for direct range restriction require three assumptions: (1) the criterion variable is missing at random; (2) a linear relationship between independent and dependent variables; and (3) constant error variance or homoscedasticity. The results in this paper demonstrate that the standard approach for correcting restricted correlations is severely biased in cases of extreme monotone quadratic nonlinearity and heteroscedasticity. This paper offers at least three significant contributions to the existing literature. First, a method from the econometrics literature is adapted to provide more accurate estimates of unrestricted correlations. Second, derivations establish bounds on the degree of bias attributed to quadratic functions under the assumption of a monotonic relationship between test scores and criterion measurements. New results are presented on the bias associated with using the standard range restriction correction formula, and the results show that the standard correction formula yields estimates of unrestricted correlations that deviate by as much as 0.2 for high to moderate selectivity. Third, Monte Carlo simulation results demonstrate that the new procedure for correcting restricted correlations provides more accurate estimates in the presence of quadratic and heteroscedastic test score and criterion relationships.

Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in Brachypodium distachyon.

PubMed

Niu, Xin; Guan, Yuxiang; Chen, Shoukun; Li, Haifeng

2017-08-15

As a superfamily of transcription factors (TFs), the basic helix-loop-helix (bHLH) proteins have been characterized functionally in many plants with a vital role in the regulation of diverse biological processes including growth, development, response to various stresses, and so on. However, no systemic analysis of the bHLH TFs has been reported in Brachypodium distachyon, an emerging model plant in Poaceae. A total of 146 bHLH TFs were identified in the Brachypodium distachyon genome and classified into 24 subfamilies. BdbHLHs in the same subfamily share similar protein motifs and gene structures. Gene duplication events showed a close relationship to rice, maize and sorghum, and segment duplications might play a key role in the expansion of this gene family. The amino acid sequence of the bHLH domains were quite conservative, especially Leu-27 and Leu-54. Based on the predicted binding activities, the BdbHLHs were divided into DNA binding and non-DNA binding types. According to the gene ontology (GO) analysis, BdbHLHs were speculated to function in homodimer or heterodimer manner. By integrating the available high throughput data in public database and results of quantitative RT-PCR, we found the expression profiles of BdbHLHs were different, implying their differentiated functions. One hundred fourty-six BdbHLHs were identified and their conserved domains, sequence features, phylogenetic relationship, chromosomal distribution, GO annotations, gene structures, gene duplication and expression profiles were investigated. Our findings lay a foundation for further evolutionary and functional elucidation of BdbHLH genes.

Basic Helix-Loop-Helix Transcription Factors JASMONATE-ASSOCIATED MYC2-LIKE1 (JAM1), JAM2, and JAM3 Are Negative Regulators of Jasmonate Responses in Arabidopsis1[W][OPEN

PubMed Central

Sasaki-Sekimoto, Yuko; Jikumaru, Yusuke; Obayashi, Takeshi; Saito, Hikaru; Masuda, Shinji; Kamiya, Yuji; Ohta, Hiroyuki; Shirasu, Ken

2013-01-01

Jasmonates regulate transcriptional reprogramming during growth, development, and defense responses. Jasmonoyl-isoleucine, an amino acid conjugate of jasmonic acid (JA), is perceived by the protein complex composed of the F-box protein CORONATINE INSENSITIVE1 (COI1) and JASMONATE ZIM DOMAIN (JAZ) proteins, leading to the ubiquitin-dependent degradation of JAZ proteins. This activates basic helix-loop-helix-type MYC transcription factors to regulate JA-responsive genes. Here, we show that the expression of genes encoding other basic helix-loop-helix transcription factors, JASMONATE ASSOCIATED MYC2-LIKE1 (JAM1), JAM2, and JAM3, is positively regulated in a COI1- and MYC2-dependent manner in Arabidopsis (Arabidopsis thaliana). However, contrary to myc2, the jam1jam2jam3 triple mutant exhibited shorter roots when treated with methyl jasmonate (MJ), indicating enhanced responsiveness to JA. Our genome-wide expression analyses revealed that key jasmonate metabolic genes as well as a set of genes encoding transcription factors that regulate the JA-responsive metabolic genes are negatively regulated by JAMs after MJ treatment. Consistently, loss of JAM genes resulted in higher accumulation of anthocyanin in MJ-treated plants as well as higher accumulation of JA and 12-hydroxyjasmonic acid in wounded plants. These results show that JAMs negatively regulate the JA responses in a manner that is mostly antagonistic to MYC2. PMID:23852442

Equilibrium shift in solution: molecular shape recognition and precipitation of a synthetic double helix using helicene-grafted silica nanoparticles.

PubMed

Miyagawa, Masamichi; Ichinose, Wataru; Yamaguchi, Masahiko

2014-01-27

Chiral silica nanoparticles (70 nm) grafted with (P)-helicene recognized the molecular shape of double helix and random coil (P)-ethynylhelicene oligomers in solution. A mixture of the (P)-nanoparticles and double helix precipitated much faster than a mixture of the (P)-nanoparticles and random coil, and the precipitate contained only the double helix. The mixture of the (P)-nanoparticles and (P)-ethynylhelicene pentamer reversibly dispersed in trifluoromethylbenzene upon heating at 70 °C and precipitated upon cooling at 25 °C. When a 10:90 equilibrium mixture of the double helix and random coil in solution was treated with the (P)-nanoparticles, the double helix was precipitated in 53% yield and was accompanied by equilibrium shift. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Repressed expression of a gene for a basic helix-loop-helix protein causes a white flower phenotype in carnation

PubMed Central

Totsuka, Akane; Okamoto, Emi; Miyahara, Taira; Kouno, Takanobu; Cano, Emilio A.; Sasaki, Nobuhiro; Watanabe, Aiko; Tasaki, Keisuke; Nishihara, Masahiro; Ozeki, Yoshihiro

2018-01-01

In a previous study, two genes responsible for white flower phenotypes in carnation were identified. These genes encoded enzymes involved in anthocyanin synthesis, namely, flavanone 3-hydroxylase (F3H) and dihydroflavonol 4-reductase (DFR), and showed reduced expression in the white flower phenotypes. Here, we identify another candidate gene for white phenotype in carnation flowers using an RNA-seq analysis followed by RT-PCR. This candidate gene encodes a transcriptional regulatory factor of the basic helix-loop-helix (bHLH) type. In the cultivar examined here, both F3H and DFR genes produced active enzyme proteins; however, expression of DFR and of genes for enzymes involved in the downstream anthocyanin synthetic pathway from DFR was repressed in the absence of bHLH expression. Occasionally, flowers of the white flowered cultivar used here have red speckles and stripes on the white petals. We found that expression of bHLH occurred in these red petal segments and induced expression of DFR and the following downstream enzymes. Our results indicate that a member of the bHLH superfamily is another gene involved in anthocyanin synthesis in addition to structural genes encoding enzymes. PMID:29681756

Classification and evolutionary analysis of the basic helix-loop-helix gene family in the green anole lizard, Anolis carolinensis.

PubMed

Liu, Ake; Wang, Yong; Zhang, Debao; Wang, Xuhua; Song, Huifang; Dang, Chunwang; Yao, Qin; Chen, Keping

2013-08-01

Helix-loop-helix (bHLH) proteins play essential regulatory roles in a variety of biological processes. These highly conserved proteins form a large transcription factor superfamily, and are commonly identified in large numbers within animal, plant, and fungal genomes. The bHLH domain has been well studied in many animal species, but has not yet been characterized in non-avian reptiles. In this study, we identified 102 putative bHLH genes in the genome of the green anole lizard, Anolis carolinensis. Based on phylogenetic analysis, these genes were classified into 43 families, with 43, 24, 16, 3, 10, and 3 members assigned into groups A, B, C, D, E, and F, respectively, and 3 members categorized as "orphans". Within-group evolutionary relationships inferred from the phylogenetic analysis were consistent with highly conserved patterns observed for introns and additional domains. Results from phylogenetic analysis of the H/E(spl) family suggest that genome and tandem gene duplications have contributed to this family's expansion. Our classification and evolutionary analysis has provided insights into the evolutionary diversification of animal bHLH genes, and should aid future studies on bHLH protein regulation of key growth and developmental processes.

The Effect of C-Terminal Helix on the Stability of FF Domain Studied by Molecular Dynamics Simulation

PubMed Central

Zhao, Liling; Cao, Zanxia; Wang, Jihua

2012-01-01

To investigate the effect of C-terminal helix on the stability of the FF domain, we studied the native domain FF3-71 from human HYPA/FBP11 and the truncated version FF3-60 with C-terminal helix being deleted by molecular dynamics simulations with GROMACS package and GROMOS 43A1 force field. The results indicated that the structures of truncated version FF3-60 were evident different from those of native partner FF3-71. Compared with FF3-71, the FF3-60 lost some native contacts and exhibited some similar structural characters to those of intermediate state. The C-terminal helix played a major role in stabilizing the FF3-71 domain. To a certain degree, the FF domain had a tendency to form an intermediate state without the C-terminal helix. In our knowledge, this was the first study to examine the role of C-terminal helix of FF domain in detail by molecular dynamics simulations, which was useful to understand the three-state folding mechanism of the small FF domain. PMID:22408419

Smoothing optimization of supporting quadratic surfaces with Zernike polynomials

NASA Astrophysics Data System (ADS)

Zhang, Hang; Lu, Jiandong; Liu, Rui; Ma, Peifu

2018-03-01

A new optimization method to get a smooth freeform optical surface from an initial surface generated by the supporting quadratic method (SQM) is proposed. To smooth the initial surface, a 9-vertex system from the neighbor quadratic surface and the Zernike polynomials are employed to establish a linear equation system. A local optimized surface to the 9-vertex system can be build by solving the equations. Finally, a continuous smooth optimization surface is constructed by stitching the above algorithm on the whole initial surface. The spot corresponding to the optimized surface is no longer discrete pixels but a continuous distribution.

Helix-Grafted Pleckstrin Homology Domains Suppress HIV-1 Infection of CD4-Positive Cells.

PubMed

Tennyson, Rachel L; Walker, Susanne N; Ikeda, Terumasa; Harris, Reuben S; Kennan, Alan J; McNaughton, Brian R

2016-10-17

The size, functional group diversity and three-dimensional structure of proteins often allow these biomolecules to bind disease-relevant structures that challenge or evade small-molecule discovery. Additionally, folded proteins are often much more stable in biologically relevant environments compared to their peptide counterparts. We recently showed that helix-grafted display-extensive resurfacing and elongation of an existing solvent-exposed helix in a pleckstrin homology (PH) domain-led to a new protein that binds a surrogate of HIV-1 gp41, a validated target for inhibition of HIV-1 entry. Expanding on this work, we prepared a number of human-derived helix-grafted-display PH domains of varied helix length and measured properties relevant to therapeutic and basic research applications. In particular, we showed that some of these new reagents expressed well as recombinant proteins in Escherichia coli, were relatively stable in human serum, bound a mimic of pre-fusogenic HIV-1 gp41 in vitro and in complex biological environments, and significantly lowered the incidence of HIV-1 infection of CD4-positive cells. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Estimating factors influencing the detection probability of semiaquatic freshwater snails using quadrat survey methods

USGS Publications Warehouse

Roesler, Elizabeth L.; Grabowski, Timothy B.

2018-01-01

Developing effective monitoring methods for elusive, rare, or patchily distributed species requires extra considerations, such as imperfect detection. Although detection is frequently modeled, the opportunity to assess it empirically is rare, particularly for imperiled species. We used Pecos assiminea (Assiminea pecos), an endangered semiaquatic snail, as a case study to test detection and accuracy issues surrounding quadrat searches. Quadrats (9 × 20 cm; n = 12) were placed in suitable Pecos assiminea habitat and randomly assigned a treatment, defined as the number of empty snail shells (0, 3, 6, or 9). Ten observers rotated through each quadrat, conducting 5-min visual searches for shells. The probability of detecting a shell when present was 67.4 ± 3.0%, but it decreased with the increasing litter depth and fewer number of shells present. The mean (± SE) observer accuracy was 25.5 ± 4.3%. Accuracy was positively correlated to the number of shells in the quadrat and negatively correlated to the number of times a quadrat was searched. The results indicate quadrat surveys likely underrepresent true abundance, but accurately determine the presence or absence. Understanding detection and accuracy of elusive, rare, or imperiled species improves density estimates and aids in monitoring and conservation efforts.

Photon-phonon parametric oscillation induced by quadratic coupling in an optomechanical resonator

NASA Astrophysics Data System (ADS)

Zhang, Lin; Ji, Fengzhou; Zhang, Xu; Zhang, Weiping

2017-07-01

A direct photon-phonon parametric effect of quadratic coupling on the mean-field dynamics of an optomechanical resonator in the large-scale-movement regime is found and investigated. Under a weak pumping power, the mechanical resonator damps to a steady state with a nonlinear static response sensitively modified by the quadratic coupling. When the driving power increases beyond the static energy balance, the steady states lose their stabilities via Hopf bifurcations, and the resonator produces stable self-sustained oscillation (limit-circle behavior) of discrete energies with step-like amplitudes due to the parametric effect of quadratic coupling, which can be understood roughly by the power balance between gain and loss on the resonator. A further increase in the pumping power can induce a chaotic dynamic of the resonator via a typical routine of period-doubling bifurcation, but which can be stabilized by the parametric effect through an inversion-bifurcation process back to the limit-circle states. The bifurcation-to-inverse-bifurcation transitions are numerically verified by the maximal Lyapunov exponents of the dynamics, which indicate an efficient way of suppressing the chaotic behavior of the optomechanical resonator by quadratic coupling. Furthermore, the parametric effect of quadratic coupling on the dynamic transitions of an optomechanical resonator can be conveniently detected or traced by the output power spectrum of the cavity field.

The discovery of the -helix and -sheet, the principal structural features of proteins

NASA Astrophysics Data System (ADS)

Eisenberg, David

2003-09-01

PNAS papers by Linus Pauling, Robert Corey, and Herman Branson in the spring of 1951 proposed the -helix and the -sheet, now known to form the backbones of tens of thousands of proteins. They deduced these fundamental building blocks from properties of small molecules, known both from crystal structures and from Pauling's resonance theory of chemical bonding that predicted planar peptide groups. Earlier attempts by others to build models for protein helices had failed both by including nonplanar peptides and by insisting on helices with an integral number of units per turn. In major respects, the Pauling-Corey-Branson models were astoundingly correct, including bond lengths that were not surpassed in accuracy for >40 years. However, they did not consider the hand of the helix or the possibility of bent sheets. They also proposed structures and functions that have not been found, including the -helix.

Curious Consequences of a Miscopied Quadratic

ERIC Educational Resources Information Center

Poet, Jeffrey L.; Vestal, Donald L., Jr.

2005-01-01

The starting point of this article is a search for pairs of quadratic polynomials x[superscript 2] + bx plus or minus c with the property that they both factor over the integers. The search leads quickly to some number theory in the form of primitive Pythagorean triples, and this paper develops the connection between these two topics.

Self-assembled RNA-triple-helix hydrogel scaffold for microRNA modulation in the tumour microenvironment

NASA Astrophysics Data System (ADS)

Conde, João; Oliva, Nuria; Atilano, Mariana; Song, Hyun Seok; Artzi, Natalie

2016-03-01

The therapeutic potential of miRNA (miR) in cancer is limited by the lack of efficient delivery vehicles. Here, we show that a self-assembled dual-colour RNA-triple-helix structure comprising two miRNAs--a miR mimic (tumour suppressor miRNA) and an antagomiR (oncomiR inhibitor)--provides outstanding capability to synergistically abrogate tumours. Conjugation of RNA triple helices to dendrimers allows the formation of stable triplex nanoparticles, which form an RNA-triple-helix adhesive scaffold upon interaction with dextran aldehyde, the latter able to chemically interact and adhere to natural tissue amines in the tumour. We also show that the self-assembled RNA-triple-helix conjugates remain functional in vitro and in vivo, and that they lead to nearly 90% levels of tumour shrinkage two weeks post-gel implantation in a triple-negative breast cancer mouse model. Our findings suggest that the RNA-triple-helix hydrogels can be used as an efficient anticancer platform to locally modulate the expression of endogenous miRs in cancer.

Strong contributions from vertical triads to helix-partner preferences in parallel coiled coils.

PubMed

Steinkruger, Jay D; Bartlett, Gail J; Woolfson, Derek N; Gellman, Samuel H

2012-09-26

Pairing preferences in heterodimeric coiled coils are determined by complementarities among side chains that pack against one another at the helix-helix interface. However, relationships between dimer stability and interfacial residue identity are not fully understood. In the context of the "knobs-into-holes" (KIH) packing pattern, one can identify two classes of interactions between side chains from different helices: "lateral", in which a line connecting the adjacent side chains is perpendicular to the helix axes, and "vertical", in which the connecting line is parallel to the helix axes. We have previously analyzed vertical interactions in antiparallel coiled coils and found that one type of triad constellation (a'-a-a') exerts a strong effect on pairing preferences, while the other type of triad (d'-d-d') has relatively little impact on pairing tendencies. Here, we ask whether vertical interactions (d'-a-d') influence pairing in parallel coiled-coil dimers. Our results indicate that vertical interactions can exert a substantial impact on pairing specificity, and that the influence of the d'-a-d' triad depends on the lateral a' contact within the local KIH motif. Structure-informed bioinformatic analyses of protein sequences reveal trends consistent with the thermodynamic data derived from our experimental model system in suggesting that heterotriads involving Leu and Ile are preferred over homotriads involving Leu and Ile.

Chandra Detects Enigmatic Point X-ray Sources in the Cat's Eye and the Helix Nebulae

NASA Astrophysics Data System (ADS)

Guerrero, M. A.; Gruendl, R. A.; Chu, Y.-H.; Kaler, J. B.; Williams, R. M.

2000-12-01

Central stars of planetary nebulae (PNe) with Teff greater than 100,000 K are expected to emit soft X-rays that peak below 0.1 keV. Chandra ACIS-S observations of the Cat's Eye Nebula (NGC 6543) and the Helix Nebula (NGC 7293) have detected point X-ray sources at their central stars. The point X-ray source at the central star of the Cat's Eye is both unknown previously and unexpected because the stellar temperature is only ~50,000 K. In contrast, the point X-ray source at the central star of the Helix was previously detected by ROSAT and its soft X-ray emission is expected because the stellar temperature is ~100,000 K. However, the Helix X-ray source also shows a harder X-ray component peaking at 0.8 keV that is unexpected and for which Chandra has provided the first high-resolution spectrum for detailed analysis. The spectra of the point X-ray sources in the Cat's Eye and the Helix show line features indicating an origin of thermal plasma emission. The spectrum of the Helix source can be fit by Raymond & Smith's model of plasma emission at ~9*E6 K. The spectrum of the Cat's Eye source has too few counts for a spectral fit, but appears to be consistent with plasma emission at 2-3*E6 K. The X-ray luminosities of both sources are ~5*E29 erg s-1. The observed plasma temperatures are too high for accretion disks around white dwarfs, but they could be ascribed to coronal X-ray emission. While central stars of PNe are not known to have coronae, the observed spectra are consistent with quiescent X-ray emission from dM flare stars. On the other hand, neither the central star of the Helix or the Cat's Eye are known to have a binary companion. It is possible that the X-rays from the Cat's Eye's central star originate from shocks in the stellar wind, but the central star of the Helix does not have a measurable fast stellar wind. This work is supported by the CXC grant number GO0-1004X.

A rare polyglycine type II-like helix motif in naturally occurring proteins.

PubMed

Warkentin, Eberhard; Weidenweber, Sina; Schühle, Karola; Demmer, Ulrike; Heider, Johann; Ermler, Ulrich

2017-11-01

Common structural elements in proteins such as α-helices or β-sheets are characterized by uniformly repeating, energetically favorable main chain conformations which additionally exhibit a completely saturated hydrogen-bonding network of the main chain NH and CO groups. Although polyproline or polyglycine type II helices (PP II or PG II ) are frequently found in proteins, they are not considered as equivalent secondary structure elements because they do not form a similar self-contained hydrogen-bonding network of the main chain atoms. In this context our finding of an unusual motif of glycine-rich PG II -like helices in the structure of the acetophenone carboxylase core complex is of relevance. These PG II -like helices form hexagonal bundles which appear to fulfill the criterion of a (largely) saturated hydrogen-bonding network of the main-chain groups and therefore may be regarded in this sense as a new secondary structure element. It consists of a central PG II -like helix surrounded by six nearly parallel PG II -like helices in a hexagonal array, plus an additional PG II -like helix extending the array outwards. Very related structural elements have previously been found in synthetic polyglycine fibers. In both cases, all main chain NH and CO groups of the central PG II -helix are saturated by either intra- or intermolecular hydrogen-bonds, resulting in a self-contained hydrogen-bonding network. Similar, but incomplete PG II -helix patterns were also previously identified in a GTP-binding protein and an antifreeze protein. © 2017 Wiley Periodicals, Inc.

Evaluating the efficiency of a one-square-meter quadrat sampler for riffle-dwelling fish

USGS Publications Warehouse

Peterson, J.T.; Rabeni, C.F.

2001-01-01

We evaluated the efficacy of a 1-m2 quadrat sampler for collecting riffle-dwelling fishes in an Ozark stream. We used a dual-gear approach to evaluate sampler efficiency in relation to species, fish size, and habitat variables. Quasi-likelihood regression showed sampling efficiency to differ significantly (P 0.05). Sampling efficiency was significantly influenced by physical habitat characteristics. Mean current velocity negatively influenced sampling efficiencies for Cyprinidae (P = 0.009), Cottidae (P = 0.006), and Percidae (P < 0.001), and the amount of cobble substrate negatively influenced sampling efficiencies for Cyprinidae (P = 0.025), Ictaluridae (P < 0.001), and Percidae (P < 0.001). Water temperature negatively influenced sampling efficiency for Cyprinidae (P = 0.009) and Ictaluridae (P = 0.006). Species-richness efficiency was positively influenced (P = 0.002) by percentage of riffle sampled. Under average habitat conditions encountered in stream riffles, the 1-m2 quadrat sampler was most efficient at estimating the densities of Cyprinidae (84%) and Cottidae (80%) and least efficient for Percidae (57%) and Ictaluridae (31%).

A single peptide loop in an alpha-Helix

USDA-ARS?s Scientific Manuscript database

Pitch is not a height but a ratio of rise/run. In an alpha-helix, run can be as the radius (r) from the center of the circle, as a diameter (d) measured across/bisecting a circumference, or as a distance (c) along a circumference; rise in each case can corresponds to same height (h) increase. For ...

A Bayesian Model for the Estimation of Latent Interaction and Quadratic Effects When Latent Variables Are Non-Normally Distributed

ERIC Educational Resources Information Center

Kelava, Augustin; Nagengast, Benjamin

2012-01-01

Structural equation models with interaction and quadratic effects have become a standard tool for testing nonlinear hypotheses in the social sciences. Most of the current approaches assume normally distributed latent predictor variables. In this article, we present a Bayesian model for the estimation of latent nonlinear effects when the latent…

Persistent spin helix manipulation by optical doping of a CdTe quantum well

NASA Astrophysics Data System (ADS)

Passmann, F.; Anghel, S.; Tischler, T.; Poshakinskiy, A. V.; Tarasenko, S. A.; Karczewski, G.; Wojtowicz, T.; Bristow, A. D.; Betz, M.

2018-05-01

Time-resolved Kerr-rotation microscopy explores the influence of optical doping on the persistent spin helix in a [001]-grown CdTe quantum well at cryogenic temperatures. Electron spin-diffusion dynamics reveal a momentum-dependent effective magnetic field providing SU(2) spin-rotation symmetry, consistent with kinetic theory. The Dresselhaus and Rashba spin-orbit coupling parameters are extracted independently from rotating the spin helix with external magnetic fields applied parallel and perpendicular to the effective magnetic field. Most importantly, a nonuniform spatiotemporal precession pattern is observed. The kinetic-theory framework of spin diffusion allows for modeling of this finding by incorporating the photocarrier density into the Rashba (α) and the Dresselhaus (β3) parameters. Corresponding calculations are further validated by an excitation-density-dependent measurement. This work shows universality of the persistent spin helix by its observation in a II-VI compound and the ability to fine-tune it by optical doping.

Exponential Thurston maps and limits of quadratic differentials

NASA Astrophysics Data System (ADS)

Hubbard, John; Schleicher, Dierk; Shishikura, Mitsuhiro

2009-01-01

We give a topological characterization of postsingularly finite topological exponential maps, i.e., universal covers g\\colon{C}to{C}setminus\\{0\\} such that 0 has a finite orbit. Such a map either is Thurston equivalent to a unique holomorphic exponential map λ e^z or it has a topological obstruction called a degenerate Levy cycle. This is the first analog of Thurston's topological characterization theorem of rational maps, as published by Douady and Hubbard, for the case of infinite degree. One main tool is a theorem about the distribution of mass of an integrable quadratic differential with a given number of poles, providing an almost compact space of models for the entire mass of quadratic differentials. This theorem is given for arbitrary Riemann surfaces of finite type in a uniform way.

Some Comments on the Use of de Moivre's Theorem to Solve Quadratic Equations with Real or Complex Coefficients

ERIC Educational Resources Information Center

Bardell, Nicholas S.

2014-01-01

This paper describes how a simple application of de Moivre's theorem may be used to not only find the roots of a quadratic equation with real or generally complex coefficients but also to pinpoint their location in the Argand plane. This approach is much simpler than the comprehensive analysis presented by Bardell (2012, 2014), but it does not…

Triple Helix Formation in a Topologically Controlled DNA Nanosystem.

PubMed

Yamagata, Yutaro; Emura, Tomoko; Hidaka, Kumi; Sugiyama, Hiroshi; Endo, Masayuki

2016-04-11

In the present study, we demonstrate single-molecule imaging of triple helix formation in DNA nanostructures. The binding of the single-molecule third strand to double-stranded DNA in a DNA origami frame was examined using two different types of triplet base pairs. The target DNA strand and the third strand were incorporated into the DNA frame, and the binding of the third strand was controlled by the formation of Watson-Crick base pairing. Triple helix formation was monitored by observing the structural changes in the incorporated DNA strands. It was also examined using a photocaged third strand wherein the binding of the third strand was directly observed using high-speed atomic force microscopy during photoirradiation. We found that the binding of the third strand could be controlled by regulating duplex formation and the uncaging of the photocaged strands in the designed nanospace. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Genome-Wide Identification of Basic Helix-Loop-Helix Motifs in Pediculus humanus corporis (Phthiraptera: Pediculidae)

PubMed Central

Wang, Xu-Hua; Wang, Yong; Zhang, De-Bao; Liu, A-Ke; Yao, Qin; Chen, Ke-Ping

2014-01-01

Abstract Basic helix-loop-helix (bHLH) proteins comprise a large superfamily of transcription factors, which are involved in the regulation of various developmental processes. bHLH family members are widely distributed in various eukaryotes including yeast, fruit fly, zebrafish, mouse, and human. In this study, we identified 55 bHLH motifs encoded in genome sequence of the human body louse, Pediculus humanus corporis (Phthiraptera: Pediculidae). Phylogenetic analyses of the identified P. humanus corporis bHLH (PhcbHLH) motifs revealed that there are 23, 11, 9, 1, 10, and 1 member(s) in groups A, B, C, D, E, and F, respectively. Examination to GenBank annotations of the 55 PhcbHLH members indicated that 29 PhcbHLH proteins were annotated in consistence with our analytical result, 8 were annotated different with our analytical result, 12 were merely annotated as hypothetical protein, and the rest 6 were not deposited in GenBank. A comparison on insect bHLH gene composition revealed that human body louse possibly has more hairy and E(spl) genes than other insect species. Because hairy and E(spl) genes have been found to negatively regulate the differentiation of insect preneural cells, it is suggested that the existence of additional hairy and E(spl) genes in human body louse is probably the consequence of its long period adaptation to the relatively dark and stable environment. These data provide good references for further studies on regulatory functions of bHLH proteins in the growth and development of human body louse. PMID:25434030

Quadratic RK shooting solution for a environmental parameter prediction boundary value problem

NASA Astrophysics Data System (ADS)

Famelis, Ioannis Th.; Tsitouras, Ch.

2014-10-01

Using tools of Information Geometry, the minimum distance between two elements of a statistical manifold is defined by the corresponding geodesic, e.g. the minimum length curve that connects them. Such a curve, where the probability distribution functions in the case of our meteorological data are two parameter Weibull distributions, satisfies a 2nd order Boundary Value (BV) system. We study the numerical treatment of the resulting special quadratic form system using Shooting method. We compare the solutions of the problem when we employ a classical Singly Diagonally Implicit Runge Kutta (SDIRK) 4(3) pair of methods and a quadratic SDIRK 5(3) pair . Both pairs have the same computational costs whereas the second one attains higher order as it is specially constructed for quadratic problems.

Iridescent Glory of Nearby Helix Nebula

NASA Image and Video Library

2014-04-04

This composite picture is a seamless blend of ultra-sharp NASA Hubble Space Telescope (HST) images combined with the wide view of the Mosaic Camera on the National Science Foundation's 0.9-meter telescope at Kitt Peak National Observatory, part of the National Optical Astronomy Observatory, near Tucson, Ariz. Astronomers at the Space Telescope Science Institute assembled these images into a mosaic. The mosaic was then blended with a wider photograph taken by the Mosaic Camera. The image shows a fine web of filamentary "bicycle-spoke" features embedded in the colorful red and blue gas ring, which is one of the nearest planetary nebulae to Earth. Because the nebula is nearby, it appears as nearly one-half the diameter of the full Moon. This required HST astronomers to take several exposures with the Advanced Camera for Surveys to capture most of the Helix. HST views were then blended with a wider photo taken by the Mosaic Camera. The portrait offers a dizzying look down what is actually a trillion-mile-long tunnel of glowing gases. The fluorescing tube is pointed nearly directly at Earth, so it looks more like a bubble than a cylinder. A forest of thousands of comet-like filaments, embedded along the inner rim of the nebula, points back toward the central star, which is a small, super-hot white dwarf. The tentacles formed when a hot "stellar wind" of gas plowed into colder shells of dust and gas ejected previously by the doomed star. Ground-based telescopes have seen these comet-like filaments for decades, but never before in such detail. The filaments may actually lie in a disk encircling the hot star, like a collar. The radiant tie-die colors correspond to glowing oxygen (blue) and hydrogen and nitrogen (red). Valuable Hubble observing time became available during the November 2002 Leonid meteor storm. To protect the spacecraft, including HST's precise mirror, controllers turned the aft end into the direction of the meteor stream for about half a day. Fortunately

Exact solutions for an oscillator with anti-symmetric quadratic nonlinearity

NASA Astrophysics Data System (ADS)

Beléndez, A.; Martínez, F. J.; Beléndez, T.; Pascual, C.; Alvarez, M. L.; Gimeno, E.; Arribas, E.

2018-04-01

Closed-form exact solutions for an oscillator with anti-symmetric quadratic nonlinearity are derived from the first integral of the nonlinear differential equation governing the behaviour of this oscillator. The mathematical model is an ordinary second order differential equation in which the sign of the quadratic nonlinear term changes. Two parameters characterize this oscillator: the coefficient of the linear term and the coefficient of the quadratic term. Not only the common case in which both coefficients are positive but also all possible combinations of positive and negative signs of these coefficients which provide periodic motions are considered, giving rise to four different cases. Three different periods and solutions are obtained, since the same result is valid in two of these cases. An interesting feature is that oscillatory motions whose equilibrium points are not at x = 0 are also considered. The periods are given in terms of an incomplete or complete elliptic integral of the first kind, and the exact solutions are expressed as functions including Jacobi elliptic cosine or sine functions.

Extended Decentralized Linear-Quadratic-Gaussian Control

NASA Technical Reports Server (NTRS)

Carpenter, J. Russell

2000-01-01

A straightforward extension of a solution to the decentralized linear-Quadratic-Gaussian problem is proposed that allows its use for commonly encountered classes of problems that are currently solved with the extended Kalman filter. This extension allows the system to be partitioned in such a way as to exclude the nonlinearities from the essential algebraic relationships that allow the estimation and control to be optimally decentralized.

Quadratic grating apodized photon sieves for simultaneous multiplane microscopy

NASA Astrophysics Data System (ADS)

Cheng, Yiguang; Zhu, Jiangping; He, Yu; Tang, Yan; Hu, Song; Zhao, Lixin

2017-10-01

We present a new type of imaging device, named quadratic grating apodized photon sieve (QGPS), used as the objective for simultaneous multiplane imaging in X-rays. The proposed QGPS is structured based on the combination of two concepts: photon sieves and quadratic gratings. Its design principles are also expounded in detail. Analysis of imaging properties of QGPS in terms of point-spread function shows that QGPS can image multiple layers within an object field onto a single image plane. Simulated and experimental results in visible light both demonstrate the feasibility of QGPS for simultaneous multiplane imaging, which is extremely promising to detect dynamic specimens by X-ray microscopy in the physical and life sciences.

Investigating Students' Mathematical Difficulties with Quadratic Equations

ERIC Educational Resources Information Center

O'Connor, Bronwyn Reid; Norton, Stephen

2016-01-01

This paper examines the factors that hinder students' success in working with and understanding the mathematics of quadratic equations using a case study analysis of student error patterns. Twenty-five Year 11 students were administered a written test to examine their understanding of concepts and procedures associated with this topic. The…

Theoretical Design Study of a 2-18 GHz Bandwidth Helix TWT (Traveling Wave Tube) Amplifier

DTIC Science & Technology

1987-02-01

Inckode Security Clanification) THEORETICAL DESIGN STUDY OF A 2-18 GHz BANDWIDTH HELIX TWT AMPLIFIER 12. PERSONAL AUTNOR(S) Michael A. Frisoni 13a. TYPE...in a traveling-wave tube ( TWT ) output circuit in A’ order to realize a 2-18 GHz frequency bandwidth. The nondispersive helix circuit provides the...Input Parameters . . . . . . . . . . . 30 V. ULTRA- BROADBAND THEORY BASED ON TWT COMPUTER SIMULATION • . 33 A. Definitions

The structure of the ends of α-helices in globular proteins: effect of additional hydrogen bonds and implications for helix formation.

PubMed

Leader, David P; Milner-White, E James

2011-03-01

We prepared a set of about 2000 α-helices from a relational database of high-resolution three-dimensional structures of globular proteins, and identified additional main chain i ← i+3 hydrogen bonds at the ends of the helices (i.e., where the hydrogen bonding potential is not fulfilled by canonical i ← i+4 hydrogen bonds). About one-third of α-helices have such additional hydrogen bonds at the N-terminus, and more than half do so at the C-terminus. Although many of these additional hydrogen bonds at the C-terminus are associated with Schellman loops, the majority are not. We compared the dihedral angles at the termini of α-helices having or lacking the additional hydrogen bonds. Significant differences were found, especially at the C-terminus, where the dihedral angles at positions C2 and C1 in the absence of additional hydrogen bonds deviate substantially from those occurring within the α-helix. Using a novel approach we show how the structure of the C-terminus of the α-helix can emerge from that of constituent overlapping α-turns and β-turns, which individually show a variation in dihedral angles at different positions. We have also considered the direction of propagation of the α-helix using this approach. If one assumes that helices start as a single α-turn and grow by successive addition of further α-turns, the paths for growth in the N → C and C → N directions differ in a way that suggests that extension in the C → N direction is favored. Copyright © 2010 Wiley-Liss, Inc.

Quadratic trigonometric B-spline for image interpolation using GA

PubMed Central

Abbas, Samreen; Irshad, Misbah

2017-01-01

In this article, a new quadratic trigonometric B-spline with control parameters is constructed to address the problems related to two dimensional digital image interpolation. The newly constructed spline is then used to design an image interpolation scheme together with one of the soft computing techniques named as Genetic Algorithm (GA). The idea of GA has been formed to optimize the control parameters in the description of newly constructed spline. The Feature SIMilarity (FSIM), Structure SIMilarity (SSIM) and Multi-Scale Structure SIMilarity (MS-SSIM) indices along with traditional Peak Signal-to-Noise Ratio (PSNR) are employed as image quality metrics to analyze and compare the outcomes of approach offered in this work, with three of the present digital image interpolation schemes. The upshots show that the proposed scheme is better choice to deal with the problems associated to image interpolation. PMID:28640906

Quadratic trigonometric B-spline for image interpolation using GA.

PubMed

Hussain, Malik Zawwar; Abbas, Samreen; Irshad, Misbah

2017-01-01

In this article, a new quadratic trigonometric B-spline with control parameters is constructed to address the problems related to two dimensional digital image interpolation. The newly constructed spline is then used to design an image interpolation scheme together with one of the soft computing techniques named as Genetic Algorithm (GA). The idea of GA has been formed to optimize the control parameters in the description of newly constructed spline. The Feature SIMilarity (FSIM), Structure SIMilarity (SSIM) and Multi-Scale Structure SIMilarity (MS-SSIM) indices along with traditional Peak Signal-to-Noise Ratio (PSNR) are employed as image quality metrics to analyze and compare the outcomes of approach offered in this work, with three of the present digital image interpolation schemes. The upshots show that the proposed scheme is better choice to deal with the problems associated to image interpolation.

Feasibility of Decentralized Linear-Quadratic-Gaussian Control of Autonomous Distributed Spacecraft

NASA Technical Reports Server (NTRS)

Carpenter, J. Russell

1999-01-01

A distributed satellite formation, modeled as an arbitrary number of fully connected nodes in a network, could be controlled using a decentralized controller framework that distributes operations in parallel over the network. For such problems, a solution that minimizes data transmission requirements, in the context of linear-quadratic-Gaussian (LQG) control theory, was given by Speyer. This approach is advantageous because it is non-hierarchical, detected failures gracefully degrade system performance, fewer local computations are required than for a centralized controller, and it is optimal with respect to the standard LQG cost function. Disadvantages of the approach are the need for a fully connected communications network, the total operations performed over all the nodes are greater than for a centralized controller, and the approach is formulated for linear time-invariant systems. To investigate the feasibility of the decentralized approach to satellite formation flying, a simple centralized LQG design for a spacecraft orbit control problem is adapted to the decentralized framework. The simple design uses a fixed reference trajectory (an equatorial, Keplerian, circular orbit), and by appropriate choice of coordinates and measurements is formulated as a linear time-invariant system.

The triple helix of collagens - an ancient protein structure that enabled animal multicellularity and tissue evolution.

PubMed

Fidler, Aaron L; Boudko, Sergei P; Rokas, Antonis; Hudson, Billy G

2018-04-09

The cellular microenvironment, characterized by an extracellular matrix (ECM), played an essential role in the transition from unicellularity to multicellularity in animals (metazoans), and in the subsequent evolution of diverse animal tissues and organs. A major ECM component are members of the collagen superfamily -comprising 28 types in vertebrates - that exist in diverse supramolecular assemblies ranging from networks to fibrils. Each assembly is characterized by a hallmark feature, a protein structure called a triple helix. A current gap in knowledge is understanding the mechanisms of how the triple helix encodes and utilizes information in building scaffolds on the outside of cells. Type IV collagen, recently revealed as the evolutionarily most ancient member of the collagen superfamily, serves as an archetype for a fresh view of fundamental structural features of a triple helix that underlie the diversity of biological activities of collagens. In this Opinion, we argue that the triple helix is a protein structure of fundamental importance in building the extracellular matrix, which enabled animal multicellularity and tissue evolution. © 2018. Published by The Company of Biologists Ltd.

Trimerization and Triple Helix Stabilization of the Collagen XIX NC2 Domain*

PubMed Central

Boudko, Sergei P.; Engel, Jürgen; Bächinger, Hans Peter

2008-01-01

The mechanisms of chain selection and assembly of fibril-associated collagens with interrupted triple helices (FACITs) must differ from that of fibrillar collagens, since they lack the characteristic C-propeptide. We analyzed two carboxyl-terminal noncollagenous domains, NC2 and NC1, of collagen XIX as potential trimerization units and found that NC2 forms a stable trimer and substantially stabilizes a collagen triple helix attached to either end. In contrast, the NC1 domain requires formation of an adjacent collagen triple helix to form interchain disulfide bridges. The NC2 domain of collagen XIX and probably of other FACITs is responsible for chain selection and trimerization. PMID:18845531

Sequential design of discrete linear quadratic regulators via optimal root-locus techniques

NASA Technical Reports Server (NTRS)

Shieh, Leang S.; Yates, Robert E.; Ganesan, Sekar

1989-01-01

A sequential method employing classical root-locus techniques has been developed in order to determine the quadratic weighting matrices and discrete linear quadratic regulators of multivariable control systems. At each recursive step, an intermediate unity rank state-weighting matrix that contains some invariant eigenvectors of that open-loop matrix is assigned, and an intermediate characteristic equation of the closed-loop system containing the invariant eigenvalues is created.

Quadratic time dependent Hamiltonians and separation of variables

NASA Astrophysics Data System (ADS)

Anzaldo-Meneses, A.

2017-06-01

Time dependent quantum problems defined by quadratic Hamiltonians are solved using canonical transformations. The Green's function is obtained and a comparison with the classical Hamilton-Jacobi method leads to important geometrical insights like exterior differential systems, Monge cones and time dependent Gaussian metrics. The Wei-Norman approach is applied using unitary transformations defined in terms of generators of the associated Lie groups, here the semi-direct product of the Heisenberg group and the symplectic group. A new explicit relation for the unitary transformations is given in terms of a finite product of elementary transformations. The sequential application of adequate sets of unitary transformations leads naturally to a new separation of variables method for time dependent Hamiltonians, which is shown to be related to the Inönü-Wigner contraction of Lie groups. The new method allows also a better understanding of interacting particles or coupled modes and opens an alternative way to analyze topological phases in driven systems.

Factorization method of quadratic template

NASA Astrophysics Data System (ADS)

Kotyrba, Martin

2017-07-01

Multiplication of two numbers is a one-way function in mathematics. Any attempt to distribute the outcome to its roots is called factorization. There are many methods such as Fermat's factorization, Dixońs method or quadratic sieve and GNFS, which use sophisticated techniques fast factorization. All the above methods use the same basic formula differing only in its use. This article discusses a newly designed factorization method. Effective implementation of this method in programs is not important, it only represents and clearly defines its properties.

Quadratic forms involving Green's and Robin functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dubinin, Vladimir N

2009-10-31

General inequalities for quadratic forms with coefficients depending on the values of Green's and Robin functions are obtained. These inequalities cover also the reduced moduli of strips and half-strips. Some applications of the results obtained to extremal partitioning problems and related questions of geometric function theory are discussed. Bibliography: 29 titles.

Increased helix and protein stability through the introduction of a new tertiary hydrogen bond.

PubMed

Peterson, R W; Nicholson, E M; Thapar, R; Klevit, R E; Scholtz, J M

1999-03-12

In an effort to quantify the importance of hydrogen bonding and alpha-helix formation to protein stability, a capping box motif was introduced into the small phosphocarrier protein HPr. Previous studies had confirmed that Ser46, at the N-cap position of the short helix-B in HPr, serves as an N-cap in solution. Thus, only a single-site mutation was required to produce a canonical S-X-X-E capping box: Lys49 at the N3 position was substituted with a glutamic acid residue. Thermal and chemical denaturation studies on the resulting K49E HPr show that the designed variant is approximately 2 kcal mol-1 more stable than the wild-type protein. However, NMR studies indicate that the side-chain of Glu49 does not participate in the expected capping H-bond interaction, but instead forms a new tertiary H-bond that links helix-B to the four-stranded beta-sheet of HPr. Here, we demonstrate that a strategy in which new non-native H-bonds are introduced can generate proteins with increased stability. We discuss why the original capping box design failed, and compare the energetic consequences of the new tertiary side-chain to main-chain H-bond with a local (helix-capping) side-chain to main-chain H-bond on the protein's global stability. Copyright 1999 Academic Press.

Mechanical performance of PPy helix tube microactuator

NASA Astrophysics Data System (ADS)

Bahrami Samani, Mehrdad; Spinks, Geoffrey M.; Cook, Christopher

2004-02-01

Conducting polymer actuators with favourable properties such as linearity, high power density and compliance are of increasing demand in micro applications. These materials generate forces over two times larger than produced by mammalian skeletal muscles. They operate to convert electro chemical energy to mechanical stress and strain. On the other hand, the application of conducting polymers is limited by the lack of a full description of the relation between four essential parameters: stress, strain, voltage and current. In this paper, polypyrrole helix tube micro actuator mechanical characteristics are investigated. The electrolyte is propylene carbonate and the dopant is TBA. PF6. The experiments are both in isotonic and isometric conditions and the input parameters are both electrical and mechanical. A dual mode force and length control and potentiostat / galvanostat are utilized for this purpose. Ultimately, the viscoelastic behaviour of the actuator is presented in this paper by a standard stress relaxation test. The effect of electrical stimulus on mechanical parameters is also explored by cyclic voltametry at different scan rates to obtain the best understanding of the actuation mechanism. The results demonstrate that the linear viscoelastic model, which performed well on conducting polymer film actuators, has to be modified to explain the mechanical behaviour of PPy helix tube fibre micro actuators. Secondly, the changes in mechanical properties of PPy need to be considered when modelling electromechanical behaviour.

A genome-wide identification of basic helix-loop-helix motifs in Pediculus humanus corporis (Phthiraptera: Pediculidae).

PubMed

Wang, Xu-Hua; Wang, Yong; Zhang, De-Bao; Liu, A-Ke; Yao, Qin; Chen, Ke-Ping

2014-01-01

Basic helix-loop-helix (bHLH) proteins comprise a large superfamily of transcription factors, which are involved in the regulation of various developmental processes. bHLH family members are widely distributed in various eukaryotes including yeast, fruit fly, zebrafish, mouse, and human. In this study, we identified 55 bHLH motifs encoded in genome sequence of the human body louse, Pediculus humanus corporis (Phthiraptera: Pediculidae). Phylogenetic analyses of the identified P. humanus corporis bHLH (PhcbHLH) motifs revealed that there are 23, 11, 9, 1, 10, and 1 member(s) in groups A, B, C, D, E, and F, respectively. Examination to GenBank annotations of the 55 PhcbHLH members indicated that 29 PhcbHLH proteins were annotated in consistence with our analytical result, 8 were annotated different with our analytical result, 12 were merely annotated as hypothetical protein, and the rest 6 were not deposited in GenBank. A comparison on insect bHLH gene composition revealed that human body louse possibly has more hairy and E(spl) genes than other insect species. Because hairy and E(spl) genes have been found to negatively regulate the differentiation of insect preneural cells, it is suggested that the existence of additional hairy and E(spl) genes in human body louse is probably the consequence of its long period adaptation to the relatively dark and stable environment. These data provide good references for further studies on regulatory functions of bHLH proteins in the growth and development of human body louse. © The Author 2014. Published by Oxford University Press on behalf of the Entomological Society of America.

Molecular Probing of the HPV-16 E6 Protein Alpha Helix Binding Groove with Small Molecule Inhibitors

PubMed Central

Rietz, Anne; Petrov, Dino P.; Bartolowits, Matthew; DeSmet, Marsha; Davisson, V. Jo; Androphy, Elliot J.

2016-01-01

The human papillomavirus (HPV) HPV E6 protein has emerged as a central oncoprotein in HPV-associated cancers in which sustained expression is required for tumor progression. A majority of the E6 protein interactions within the human proteome use an alpha-helix groove interface for binding. The UBE3A/E6AP HECT domain ubiquitin ligase binds E6 at this helix-groove interface. This enables formation of a trimeric complex with p53, resulting in destruction of this tumor suppressor. While recent x-ray crystal structures are useful, examples of small molecule probes that can modulate protein interactions at this interface are limited. To develop insights useful for potential structure-based design of ligands for HPV E6, a series of 2,6-disubstituted benzopyranones were prepared and tested as competitive antagonists of E6-E6AP helix-groove interactions. These small molecule probes were used in both binding and functional assays to evaluate recognition features of the E6 protein. Evidence for an ionic functional group interaction within the helix groove was implicated by the structure-activity among the highest affinity ligands. The molecular topographies of these protein-ligand interactions were evaluated by comparing the binding and activities of single amino acid E6 mutants with the results of molecular dynamic simulations. A group of arginine residues that form a rim-cap over the E6 helix groove offer compensatory roles in binding and recognition of the small molecule probes. The flexibility and impact on the overall helix-groove shape dictated by these residues offer new insights for structure-based targeting of HPV E6. PMID:26915086

Protein Secondary Structures (alpha-helix and beta-sheet) at a Cellular Levle and Protein Fractions in Relation to Rumen Degradation Behaviours of Protein: A New Approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu,P.

2007-01-01

Studying the secondary structure of proteins leads to an understanding of the components that make up a whole protein, and such an understanding of the structure of the whole protein is often vital to understanding its digestive behaviour and nutritive value in animals. The main protein secondary structures are the {alpha}-helix and {beta}-sheet. The percentage of these two structures in protein secondary structures influences protein nutritive value, quality and digestive behaviour. A high percentage of {beta}-sheet structure may partly cause a low access to gastrointestinal digestive enzymes, which results in a low protein value. The objectives of the present studymore » were to use advanced synchrotron-based Fourier transform IR (S-FTIR) microspectroscopy as a new approach to reveal the molecular chemistry of the protein secondary structures of feed tissues affected by heat-processing within intact tissue at a cellular level, and to quantify protein secondary structures using multicomponent peak modelling Gaussian and Lorentzian methods, in relation to protein digestive behaviours and nutritive value in the rumen, which was determined using the Cornell Net Carbohydrate Protein System. The synchrotron-based molecular chemistry research experiment was performed at the National Synchrotron Light Source at Brookhaven National Laboratory, US Department of Energy. The results showed that, with S-FTIR microspectroscopy, the molecular chemistry, ultrastructural chemical make-up and nutritive characteristics could be revealed at a high ultraspatial resolution ({approx}10 {mu}m). S-FTIR microspectroscopy revealed that the secondary structure of protein differed between raw and roasted golden flaxseeds in terms of the percentages and ratio of {alpha}-helixes and {beta}-sheets in the mid-IR range at the cellular level. By using multicomponent peak modelling, the results show that the roasting reduced (P <0.05) the percentage of {alpha}-helixes (from 47.1% to 36.1%: S

Helix formation via conformation diffusion search

PubMed Central

Huang, Cheng-Yen; Getahun, Zelleka; Zhu, Yongjin; Klemke, Jason W.; DeGrado, William F.; Gai, Feng

2002-01-01

The helix-coil transition kinetics of an α-helical peptide were investigated by time-resolved infrared spectroscopy coupled with laser-induced temperature-jump initiation method. Specific isotope labeling of the amide carbonyl groups with 13C at selected residues was used to obtain site-specific information. The relaxation kinetics following a temperature jump, obtained by probing the amide I′ band of the peptide backbone, exhibit nonexponential behavior and are sensitive to both initial and final temperatures. These data are consistent with a conformation diffusion process on the folding energy landscape, in accord with a recent molecular dynamics simulation study. PMID:11867741

Computational methods for optimal linear-quadratic compensators for infinite dimensional discrete-time systems

NASA Technical Reports Server (NTRS)

Gibson, J. S.; Rosen, I. G.

1986-01-01

An abstract approximation theory and computational methods are developed for the determination of optimal linear-quadratic feedback control, observers and compensators for infinite dimensional discrete-time systems. Particular attention is paid to systems whose open-loop dynamics are described by semigroups of operators on Hilbert spaces. The approach taken is based on the finite dimensional approximation of the infinite dimensional operator Riccati equations which characterize the optimal feedback control and observer gains. Theoretical convergence results are presented and discussed. Numerical results for an example involving a heat equation with boundary control are presented and used to demonstrate the feasibility of the method.

Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics

PubMed Central

Simionato, Elena; Ledent, Valérie; Richards, Gemma; Thomas-Chollier, Morgane; Kerner, Pierre; Coornaert, David; Degnan, Bernard M; Vervoort, Michel

2007-01-01

Background Molecular and genetic analyses conducted in model organisms such as Drosophila and vertebrates, have provided a wealth of information about how networks of transcription factors control the proper development of these species. Much less is known, however, about the evolutionary origin of these elaborated networks and their large-scale evolution. Here we report the first evolutionary analysis of a whole superfamily of transcription factors, the basic helix-loop-helix (bHLH) proteins, at the scale of the whole metazoan kingdom. Results We identified in silico the putative full complement of bHLH genes in the sequenced genomes of 12 different species representative of the main metazoan lineages, including three non-bilaterian metazoans, the cnidarians Nematostella vectensis and Hydra magnipapillata and the demosponge Amphimedon queenslandica. We have performed extensive phylogenetic analyses of the 695 identified bHLHs, which has allowed us to allocate most of these bHLHs to defined evolutionary conserved groups of orthology. Conclusion Three main features in the history of the bHLH gene superfamily can be inferred from these analyses: (i) an initial diversification of the bHLHs has occurred in the pre-Cambrian, prior to metazoan cladogenesis; (ii) a second expansion of the bHLH superfamily occurred early in metazoan evolution before bilaterians and cnidarians diverged; and (iii) the bHLH complement during the evolution of the bilaterians has been remarkably stable. We suggest that these features may be extended to other developmental gene families and reflect a general trend in the evolution of the developmental gene repertoires of metazoans. PMID:17335570

Slippery interfaces: lubrication of director and helix rotation motions (Conference Presentation)

NASA Astrophysics Data System (ADS)

Yamamoto, Jun; Sakatsuji, Waki; Nishiyama, Isa

2017-02-01

Anchoring effects on the polymer films in the liquid crystal (LC) display devices plays key role to create the restoring force to the black state. However, the chiral materials with spontaneous helix, such as deformed helix mode in SmC* (DH-FLC) or the polymer stabilized blue phase (PSChBP), can recover black state by rewinding motion of the helix itself. We have invented the principle and design of slippery interfaces, which has zero anchoring force for attached LC molecules on the interfaces, and confirmed the drastic reduction of driving voltage in DH-FLC mode of SmC* (<1 order) keeping the fast switching response (tau 50 micro sec). We have reported the lateral slippery interfaces consist of the phase separated liquid phases created by tran-cis isomerization of doped azo dye. It is not enough to the complete transmission of the light(I/I0 1) by applying the typical driving voltage ( 1.0V/micro m) for current IPS panels. It is also problem that slippery interface become effective only just below the I-SmC phase transition temperature (TIC-T<20°). Here, we report new type of the vertical slippery interface realized by the spin coated swollen azo-LC gel films on the glass substrates. Under UV irradiation, trans-cis isomerization of the azo-dye co-polymerized in the azo-LC gel film, induces the vertical slippery interfaces by the disordering effect. Since the co-polymerized azo-dye cannot be dissolved into LC, the disordering effect is completely localized in the interface between swollen azo-LC gel and bulk SmC* material. Then the slippery interfaces can be stabilized over wide temperature range. We greatly improve the reduction of the driving voltage, I/Io=1, 1.0V/micro m for rather slow change of the driving voltage (tau 1msec 2.5msec pulse), I/I0=0.6, 1.5V/micro m for fast change (tau 50 micro sec, 250 micro sec pulse) by lubrication of intra and inter helix C-director rotation motions.

A Helix-Stabilizing Linker Improves Subcutaneous Bioavailability of a Helical Peptide Independent of Linker Lipophilicity.

PubMed

Zhang, Liang; Navaratna, Tejas; Thurber, Greg M

2016-07-20

Stabilized peptides address several limitations to peptide-based imaging agents and therapeutics such as poor stability and low affinity due to conformational flexibility. There is also active research in developing these compounds for intracellular drug targeting, and significant efforts have been invested to determine the effects of helix stabilization on intracellular delivery. However, much less is known about the impact on other pharmacokinetic parameters such as plasma clearance and bioavailability. We investigated the effect of different fluorescent helix-stabilizing linkers with varying lipophilicity on subcutaneous (sc) bioavailability using the glucagon-like peptide-1 (GLP-1) receptor ligand exendin as a model system. The stabilized peptides showed significantly higher protease resistance and increased bioavailability independent of linker hydrophilicity, and all subcutaneously delivered conjugates were able to successfully target the islets of Langerhans with high specificity. The lipophilic peptide variants had slower absorption and plasma clearance than their respective hydrophilic conjugates, and the absolute bioavailability was also lower likely due to the longer residence times in the skin. Their ease and efficiency make double-click helix stabilization chemistries a useful tool for increasing the bioavailability of peptide therapeutics, many of which suffer from rapid in vivo protease degradation. Helix stabilization using linkers of varying lipophilicity can further control sc absorption and clearance rates to customize plasma pharmacokinetics.

Tracheophytes Contain Conserved Orthologs of a Basic Helix-Loop-Helix Transcription Factor That Modulate ROOT HAIR SPECIFIC Genes[OPEN

PubMed Central

Cho, Hyun-Min

2017-01-01

ROOT HAIR SPECIFIC (RHS) genes, which contain the root hair-specific cis-element (RHE) in their regulatory regions, function in root hair morphogenesis. Here, we demonstrate that an Arabidopsis thaliana basic helix-loop-helix transcription factor, ROOT HAIR DEFECTVE SIX-LIKE4 (RSL4), directly binds to the RHE in vitro and in vivo, upregulates RHS genes, and stimulates root hair formation in Arabidopsis. Orthologs of RSL4 from a eudicot (poplar [Populus trichocarpa]), a monocot (rice [Oryza sativa]), and a lycophyte (Selaginella moellendorffii) each restored root hair growth in the Arabidopsis rsl4 mutant. In addition, the rice and S. moellendorffii RSL4 orthologs bound to the RHE in in vitro and in vivo assays. The RSL4 orthologous genes contain RHEs in their promoter regions, and RSL4 was able to bind to its own RHEs in vivo and amplify its own expression. This process likely provides a positive feedback loop for sustainable root hair growth. When RSL4 and its orthologs were expressed in cells in non-root-hair positions, they induced ectopic root hair growth, indicating that these genes are sufficient to specify root hair formation. Our results suggest that RSL4 mediates root hair formation by regulating RHS genes and that this mechanism is conserved throughout the tracheophyte (vascular plant) lineage. PMID:28087829

Talent Development as a University Mission: The Quadruple Helix

ERIC Educational Resources Information Center

Holm-Nielsen, Lauritz B.; Thorn, Kristian; Olesen, Jeppe Dorup; Huey, Tina

2013-01-01

In this paper, the authors discuss the rationale behind making talent development at the PhD, post-doctoral and early career levels an equal fourth pillar of the university's mission, alongside the more traditional pillars of the triple helix. Using Denmark and Aarhus University as a case study, the paper describes how increased institutional…

Quadratic electroabsorption studies of molecular motion in dye-doped polymers

NASA Astrophysics Data System (ADS)

Poga, Constantina; Kuzyk, Mark G.; Dirk, Carl W.

1993-02-01

This paper reports on quadratic electroabsorption studies of thin-film solid solutions of squarylium dye molecules in poly(methylmethacrylate) polymer with the aim of understanding the role of electronic and reorientational mechanisms in the third-order nonlinear-optical susceptibility. We present a generalized theory of the quadratic electrooptic response that includes both electronic mechanisms and molecular reorientation and show that the ratio of two independent third-order susceptibility tensor components, namely (chi) (3)3333/(chi) (3)1133, determines the relative contribution of each mechanism. Based on these theoretical results, we have designed and built an experiment that determines this ratio as a function of temperature and wavelength. Results show that at room temperature and near the first electronic transition wavelength, the response is dominated by the electronic mechanism, and that the reorientational contribution dominates when the sample is heated above its glass transition temperature. Furthermore, results show that, off-resonance, the sign of the imaginary part of the third-order susceptibility is positive. Quadratic electroabsorption is thus shown to be a versatile tool for measuring the imaginary part of the third-order nonlinear-optical susceptibility which yields information about the interaction of polymer and dopant molecule.

Algebraic-geometry approach to integrability of birational plane mappings. Integrable birational quadratic reversible mappings. I

NASA Astrophysics Data System (ADS)

Rerikh, K. V.

1998-02-01

Using classic results of algebraic geometry for birational plane mappings in plane CP 2 we present a general approach to algebraic integrability of autonomous dynamical systems in C 2 with discrete time and systems of two autonomous functional equations for meromorphic functions in one complex variable defined by birational maps in C 2. General theorems defining the invariant curves, the dynamics of a birational mapping and a general theorem about necessary and sufficient conditions for integrability of birational plane mappings are proved on the basis of a new idea — a decomposition of the orbit set of indeterminacy points of direct maps relative to the action of the inverse mappings. A general method of generating integrable mappings and their rational integrals (invariants) I is proposed. Numerical characteristics Nk of intersections of the orbits Φn- kOi of fundamental or indeterminacy points Oi ɛ O ∩ S, of mapping Φn, where O = { O i} is the set of indeterminacy points of Φn and S is a similar set for invariant I, with the corresponding set O' ∩ S, where O' = { O' i} is the set of indeterminacy points of inverse mapping Φn-1, are introduced. Using the method proposed we obtain all nine integrable multiparameter quadratic birational reversible mappings with the zero fixed point and linear projective symmetry S = CΛC-1, Λ = diag(±1), with rational invariants generated by invariant straight lines and conics. The relations of numbers Nk with such numerical characteristics of discrete dynamical systems as the Arnold complexity and their integrability are established for the integrable mappings obtained. The Arnold complexities of integrable mappings obtained are determined. The main results are presented in Theorems 2-5, in Tables 1 and 2, and in Appendix A.

Integration of the Quadratic Function and Generalization

ERIC Educational Resources Information Center

Mitsuma, Kunio

2011-01-01

We will first recall useful formulas in integration that simplify the calculation of certain definite integrals with the quadratic function. A main formula relies only on the coefficients of the function. We will then explore a geometric proof of one of these formulas. Finally, we will extend the formulas to more general cases. (Contains 3…

GTF2IRD2 is located in the Williams-Beuren syndrome critical region 7q11.23 and encodes a protein with two TFII-I-like helix-loop-helix repeats.

PubMed

Makeyev, Aleksandr V; Erdenechimeg, Lkhamsuren; Mungunsukh, Ognoon; Roth, Jutta J; Enkhmandakh, Badam; Ruddle, Frank H; Bayarsaihan, Dashzeveg

2004-07-27

Williams-Beuren syndrome (also known as Williams syndrome) is caused by a deletion of a 1.55- to 1.84-megabase region from chromosome band 7q11.23. GTF2IRD1 and GTF2I, located within this critical region, encode proteins of the TFII-I family with multiple helix-loop-helix domains known as I repeats. In the present work, we characterize a third member, GTF2IRD2, which has sequence and structural similarity to the GTF2I and GTF2IRD1 paralogs. The ORF encodes a protein with several features characteristic of regulatory factors, including two I repeats, two leucine zippers, and a single Cys-2/His-2 zinc finger. The genomic organization of human, baboon, rat, and mouse genes is well conserved. Our exon-by-exon comparison has revealed that GTF2IRD2 is more closely related to GTF2I than to GTF2IRD1 and apparently is derived from the GTF2I sequence. The comparison of GTF2I and GTF2IRD2 genes revealed two distinct regions of homology, indicating that the helix-loop-helix domain structure of the GTF2IRD2 gene has been generated by two independent genomic duplications. We speculate that GTF2I is derived from GTF2IRD1 as a result of local duplication and the further evolution of its structure was associated with its functional specialization. Comparison of genomic sequences surrounding GTF2IRD2 genes in mice and humans allows refinement of the centromeric breakpoint position of the primate-specific inversion within the Williams-Beuren syndrome critical region.

Linear quadratic regulators with eigenvalue placement in a specified region

NASA Technical Reports Server (NTRS)

Shieh, Leang S.; Dib, Hani M.; Ganesan, Sekar

1988-01-01

A linear optimal quadratic regulator is developed for optimally placing the closed-loop poles of multivariable continuous-time systems within the common region of an open sector, bounded by lines inclined at + or - pi/2k (k = 2 or 3) from the negative real axis with a sector angle of pi/2 or less, and the left-hand side of a line parallel to the imaginary axis in the complex s-plane. The design method is mainly based on the solution of a linear matrix Liapunov equation, and the resultant closed-loop system with its eigenvalues in the desired region is optimal with respect to a quadratic performance index.

Sensitivity Analysis of Linear Programming and Quadratic Programming Algorithms for Control Allocation

NASA Technical Reports Server (NTRS)

Frost, Susan A.; Bodson, Marc; Acosta, Diana M.

2009-01-01

The Next Generation (NextGen) transport aircraft configurations being investigated as part of the NASA Aeronautics Subsonic Fixed Wing Project have more control surfaces, or control effectors, than existing transport aircraft configurations. Conventional flight control is achieved through two symmetric elevators, two antisymmetric ailerons, and a rudder. The five effectors, reduced to three command variables, produce moments along the three main axes of the aircraft and enable the pilot to control the attitude and flight path of the aircraft. The NextGen aircraft will have additional redundant control effectors to control the three moments, creating a situation where the aircraft is over-actuated and where a simple relationship does not exist anymore between the required effector deflections and the desired moments. NextGen flight controllers will incorporate control allocation algorithms to determine the optimal effector commands and attain the desired moments, taking into account the effector limits. Approaches to solving the problem using linear programming and quadratic programming algorithms have been proposed and tested. It is of great interest to understand their relative advantages and disadvantages and how design parameters may affect their properties. In this paper, we investigate the sensitivity of the effector commands with respect to the desired moments and show on some examples that the solutions provided using the l2 norm of quadratic programming are less sensitive than those using the l1 norm of linear programming.

Tuning a fuzzy controller using quadratic response surfaces

NASA Technical Reports Server (NTRS)

Schott, Brian; Whalen, Thomas

1992-01-01

Response surface methodology, an alternative method to traditional tuning of a fuzzy controller, is described. An example based on a simulated inverted pendulum 'plant' shows that with (only) 15 trial runs, the controller can be calibrated using a quadratic form to approximate the response surface.

Quantum superintegrable system with a novel chain structure of quadratic algebras

NASA Astrophysics Data System (ADS)

Liao, Yidong; Marquette, Ian; Zhang, Yao-Zhong

2018-06-01

We analyse the n-dimensional superintegrable Kepler–Coulomb system with non-central terms. We find a novel underlying chain structure of quadratic algebras formed by the integrals of motion. We identify the elements for each sub-structure and obtain the algebra relations satisfied by them and the corresponding Casimir operators. These quadratic sub-algebras are realized in terms of a chain of deformed oscillators with factorized structure functions. We construct the finite-dimensional unitary representations of the deformed oscillators, and give an algebraic derivation of the energy spectrum of the superintegrable system.

Design of polymer conjugated 3-helix micelles as nanocarriers with tunable shapes.

PubMed

Ma, Dan; DeBenedictis, Elizabeth P; Lund, Reidar; Keten, Sinan

2016-11-24

Amphiphilic peptide-polymer conjugates have the ability to form stable nanoscale micelles, which show great promise for drug delivery and other applications. A recent design has utilized the end-conjugation of alkyl chains to 3-helix coiled coils to achieve amphiphilicity, combined with the side-chain conjugation of polyethylene glycol (PEG) to tune micelle size through entropic confinement forces. Here we investigate this phenomenon in depth, using coarse-grained dissipative particle dynamics (DPD) simulations in an explicit solvent and micelle theory. We analyze the conformations of PEG chains conjugated to three different positions on 3-helix bundle peptides to ascertain the degree of confinement upon assembly, as well as the ordering of the subunits making up the micelle. We discover that the micelle size and stability is dictated by a competition between the entropy of PEG chain conformations in the assembled state, as well as intermolecular cross-interactions among PEG chains that promote cohesion between neighboring conjugates. Our analyses build on the role of PEG molecular weight and conjugation site and lead to computational phase diagrams that can be used to design 3-helix micelles. This work opens pathways for the design of multifunctional micelles with tunable size, shape and stability.

Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Storrs, Richard Wood

1992-08-01

Catalytic immunoglobin fragments were studied Nuclear Magnetic Resonance spectroscopy to identify amino acid residues responsible for the catalytic activity. Small, hybrid sequence peptides were analyzed for helix propagation following covalent initiation and for activity related to the protein from which the helical sequence was derived. Hydrolysis of p-nitrophenyl carbonates and esters by specific immunoglobins is thought to involve charge complementarity. The pK of the transition state analog P-nitrophenyl phosphate bound to the immunoglobin fragment was determined by 31P-NMR to verify the juxtaposition of a positively charged amino acid to the binding/catalytic site. Optical studies of immunoglobin mediated photoreversal of cis,more » syn cyclobutane thymine dimers implicated tryptophan as the photosensitizing chromophore. Research shows the chemical environment of a single tryptophan residue is altered upon binding of the thymine dimer. This tryptophan residue was localized to within 20 Å of the binding site through the use of a nitroxide paramagnetic species covalently attached to the thymine dimer. A hybrid sequence peptide was synthesized based on the bee venom peptide apamin in which the helical residues of apamin were replaced with those from the recognition helix of the bacteriophage 434 repressor protein. Oxidation of the disufide bonds occured uniformly in the proper 1-11, 3-15 orientation, stabilizing the 434 sequence in an α-helix. The glycine residue stopped helix propagation. Helix propagation in 2,2,2-trifluoroethanol mixtures was investigated in a second hybrid sequence peptide using the apamin-derived disulfide scaffold and the S-peptide sequence. The helix-stop signal previously observed was not observed in the NMR NOESY spectrum. Helical connectivities were seen throughout the S-peptide sequence. The apamin/S-peptide hybrid binded to the S-protein (residues 21-166 of ribonuclease A) and reconstituted enzymatic activity.« less

Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Storrs, R.W.

1992-08-01

Catalytic immunoglobin fragments were studied Nuclear Magnetic Resonance spectroscopy to identify amino acid residues responsible for the catalytic activity. Small, hybrid sequence peptides were analyzed for helix propagation following covalent initiation and for activity related to the protein from which the helical sequence was derived. Hydrolysis of p-nitrophenyl carbonates and esters by specific immunoglobins is thought to involve charge complementarity. The pK of the transition state analog P-nitrophenyl phosphate bound to the immunoglobin fragment was determined by [sup 31]P-NMR to verify the juxtaposition of a positively charged amino acid to the binding/catalytic site. Optical studies of immunoglobin mediated photoreversal ofmore » cis, syn cyclobutane thymine dimers implicated tryptophan as the photosensitizing chromophore. Research shows the chemical environment of a single tryptophan residue is altered upon binding of the thymine dimer. This tryptophan residue was localized to within 20 [Angstrom] of the binding site through the use of a nitroxide paramagnetic species covalently attached to the thymine dimer. A hybrid sequence peptide was synthesized based on the bee venom peptide apamin in which the helical residues of apamin were replaced with those from the recognition helix of the bacteriophage 434 repressor protein. Oxidation of the disufide bonds occured uniformly in the proper 1-11, 3-15 orientation, stabilizing the 434 sequence in an [alpha]-helix. The glycine residue stopped helix propagation. Helix propagation in 2,2,2-trifluoroethanol mixtures was investigated in a second hybrid sequence peptide using the apamin-derived disulfide scaffold and the S-peptide sequence. The helix-stop signal previously observed was not observed in the NMR NOESY spectrum. Helical connectivities were seen throughout the S-peptide sequence. The apamin/S-peptide hybrid binded to the S-protein (residues 21-166 of ribonuclease A) and reconstituted enzymatic activity.« less

Dynamics of a localized spin excitation close to the spin-helix regime

NASA Astrophysics Data System (ADS)

Salis, Gian; Walser, Matthias; Altmann, Patrick; Reichl, Christian; Wegscheider, Werner

2014-03-01

The time evolution of a local spin excitation in a (001)-confined two-dimensional electron gas subjected to Rashba and Dresselhaus spin-orbit interactions of similar strength is investigated theoretically and compared with experimental data. Specifically, the consequences of a finite spatial extension of the initial spin polarization are studied for non-balanced Rashba and Dresselhaus terms and for finite cubic Dresselhaus spin-orbit interaction. We show that the initial out-of-plane spin polarization evolves into a helical spin pattern with a wave number that gradually approaches the value q0 of the persistent spin helix mode. In addition to an exponential decay of the spin polarization that is proportional to both the spin-orbit imbalance and the cubic Dresselhaus term, the finite width w of the spin excitation reduces the spin polarization by a factor that approaches exp(-q02w2 / 2) at longer times. This result bridges the gap between the formation of a long-lived helical spin mode and a spatially homogeneous spin decay described by the Dyakonov-Perel mechanism. This work is financially supported by NCCR QSIT.

An Amphipathic Helix Directs Cellular Membrane Curvature Sensing and Function of the BAR Domain Protein PICK1.

PubMed

Herlo, Rasmus; Lund, Viktor K; Lycas, Matthew D; Jansen, Anna M; Khelashvili, George; Andersen, Rita C; Bhatia, Vikram; Pedersen, Thomas S; Albornoz, Pedro B C; Johner, Niklaus; Ammendrup-Johnsen, Ina; Christensen, Nikolaj R; Erlendsson, Simon; Stoklund, Mikkel; Larsen, Jannik B; Weinstein, Harel; Kjærulff, Ole; Stamou, Dimitrios; Gether, Ulrik; Madsen, Kenneth L

2018-05-15

BAR domains are dimeric protein modules that sense, induce, and stabilize lipid membrane curvature. Here, we show that membrane curvature sensing (MCS) directs cellular localization and function of the BAR domain protein PICK1. In PICK1, and the homologous proteins ICA69 and arfaptin2, we identify an amphipathic helix N-terminal to the BAR domain that mediates MCS. Mutational disruption of the helix in PICK1 impaired MCS without affecting membrane binding per se. In insulin-producing INS-1E cells, super-resolution microscopy revealed that disruption of the helix selectively compromised PICK1 density on insulin granules of high curvature during their maturation. This was accompanied by reduced hormone storage in the INS-1E cells. In Drosophila, disruption of the helix compromised growth regulation. By demonstrating size-dependent binding on insulin granules, our finding highlights the function of MCS for BAR domain proteins in a biological context distinct from their function, e.g., at the plasma membrane during endocytosis. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

One-dimensional nonlinear theory for rectangular helix traveling-wave tube

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fu, Chengfang, E-mail: fchffchf@126.com; Zhao, Bo; Yang, Yudong

A 1-D nonlinear theory of a rectangular helix traveling-wave tube (TWT) interacting with a ribbon beam is presented in this paper. The RF field is modeled by a transmission line equivalent circuit, the ribbon beam is divided into a sequence of thin rectangular electron discs with the same cross section as the beam, and the charges are assumed to be uniformly distributed over these discs. Then a method of computing the space-charge field by solving Green's Function in the Cartesian Coordinate-system is fully described. Nonlinear partial differential equations for field amplitudes and Lorentz force equations for particles are solved numericallymore » using the fourth-order Runge-Kutta technique. The tube's gain, output power, and efficiency of the above TWT are computed. The results show that increasing the cross section of the ribbon beam will improve a rectangular helix TWT's efficiency and reduce the saturated length.« less

Closed-loop stability of linear quadratic optimal systems in the presence of modeling errors

NASA Technical Reports Server (NTRS)

Toda, M.; Patel, R.; Sridhar, B.

1976-01-01

The well-known stabilizing property of linear quadratic state feedback design is utilized to evaluate the robustness of a linear quadratic feedback design in the presence of modeling errors. Two general conditions are obtained for allowable modeling errors such that the resulting closed-loop system remains stable. One of these conditions is applied to obtain two more particular conditions which are readily applicable to practical situations where a designer has information on the bounds of modeling errors. Relations are established between the allowable parameter uncertainty and the weighting matrices of the quadratic performance index, thereby enabling the designer to select appropriate weighting matrices to attain a robust feedback design.

The discovery of the alpha-helix and beta-sheet, the principal structural features of proteins.

PubMed

Eisenberg, David

2003-09-30

PNAS papers by Linus Pauling, Robert Corey, and Herman Branson in the spring of 1951 proposed the alpha-helix and the beta-sheet, now known to form the backbones of tens of thousands of proteins. They deduced these fundamental building blocks from properties of small molecules, known both from crystal structures and from Pauling's resonance theory of chemical bonding that predicted planar peptide groups. Earlier attempts by others to build models for protein helices had failed both by including nonplanar peptides and by insisting on helices with an integral number of units per turn. In major respects, the Pauling-Corey-Branson models were astoundingly correct, including bond lengths that were not surpassed in accuracy for >40 years. However, they did not consider the hand of the helix or the possibility of bent sheets. They also proposed structures and functions that have not been found, including the gamma-helix.

Characterization of a Quadratic Function in Rn

ERIC Educational Resources Information Center

Xu, Conway

2010-01-01

It is proved that a scalar-valued function "f"(x) defined in "n"-dimensional space must be quadratic, if the intersection of tangent planes at x[subscript 1] and x[subscript 2] always contains the midpoint of the line joining x[subscript 1] and x[subscript 2]. This is the converse of a result of Stenlund proved in this JOURNAL in 2001.

Comets Kick up Dust in Helix Nebula

NASA Technical Reports Server (NTRS)

2007-01-01

This infrared image from NASA's Spitzer Space Telescope shows the Helix nebula, a cosmic starlet often photographed by amateur astronomers for its vivid colors and eerie resemblance to a giant eye.

The nebula, located about 700 light-years away in the constellation Aquarius, belongs to a class of objects called planetary nebulae. Discovered in the 18th century, these colorful beauties were named for their resemblance to gas-giant planets like Jupiter.

Planetary nebulae are the remains of stars that once looked a lot like our sun. When sun-like stars die, they puff out their outer gaseous layers. These layers are heated by the hot core of the dead star, called a white dwarf, and shine with infrared and visible colors. Our own sun will blossom into a planetary nebula when it dies in about five billion years.

In Spitzer's infrared view of the Helix nebula, the eye looks more like that of a green monster's. Infrared light from the outer gaseous layers is represented in blues and greens. The white dwarf is visible as a tiny white dot in the center of the picture. The red color in the middle of the eye denotes the final layers of gas blown out when the star died.

The brighter red circle in the very center is the glow of a dusty disk circling the white dwarf (the disk itself is too small to be resolved). This dust, discovered by Spitzer's infrared heat-seeking vision, was most likely kicked up by comets that survived the death of their star. Before the star died, its comets and possibly planets would have orbited the star in an orderly fashion. But when the star blew off its outer layers, the icy bodies and outer planets would have been tossed about and into each other, resulting in an ongoing cosmic dust storm. Any inner planets in the system would have burned up or been swallowed as their dying star expanded.

So far, the Helix nebula is one of only a few dead-star systems in which evidence for comet survivors has been found.

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Emotion suppression moderates the quadratic association between RSA and executive function.

PubMed

Spangler, Derek P; Bell, Martha Ann; Deater-Deckard, Kirby

2015-09-01

There is uncertainty about whether respiratory sinus arrhythmia (RSA), a cardiac marker of adaptive emotion regulation, is involved in relatively low or high executive function performance. In the present study, we investigated (a) whether RSA during rest and tasks predict both relatively low and high executive function within a larger quadratic association among the two variables, and (b) the extent to which this quadratic trend was moderated by individual differences in emotion regulation. To achieve these aims, a sample of ethnically and socioeconomically diverse women self-reported reappraisal and emotion suppression. They next experienced a 2-min resting period during which electrocardiogram (ECG) was continually assessed. In the next phase, the women completed an array of executive function and nonexecutive cognitive tasks while ECG was measured throughout. As anticipated, resting RSA showed a quadratic association with executive function that was strongest for high suppression. These results suggest that relatively high resting RSA may predict poor executive function ability when emotion regulation consumes executive control resources needed for ongoing cognitive performance. © 2015 Society for Psychophysiological Research.

Emotion suppression moderates the quadratic association between RSA and executive function

PubMed Central

Spangler, Derek P.; Bell, Martha Ann; Deater-Deckard, Kirby

2016-01-01

There is uncertainty about whether respiratory sinus arrhythmia (RSA), a cardiac marker of adaptive emotion regulation, is involved in relatively low or high executive function performance. In the present study, we investigated: (1) whether RSA during rest and tasks predict both relatively low and high executive function within a larger quadratic association among the two variables, and (2) the extent to which this quadratic trend was moderated by individual differences in emotion regulation. To achieve these aims, a sample of ethnically and socioeconomically diverse women self-reported reappraisal and emotion suppression. They next experienced a two-minute resting period during which ECG was continually assessed. In the next phase, the women completed an array of executive function and non-executive cognitive tasks while ECG was measured throughout. As anticipated, resting RSA showed a quadratic association with executive function that was strongest for high suppression. These results suggest that relatively high resting RSA may predict poor executive function ability when emotion regulation consumes executive control resources needed for ongoing cognitive performance. PMID:26018941

Clear cell hidradenocarcinoma of the ear helix: report of primary ear helix adnexal carcinoma with regional lymph node metastasis.

PubMed

Bae, Tae Hui; Kang, Shin Hyuk; Kim, Han Koo; Kim, Woo Seob; Kim, Mi Kyung

2014-07-01

Clear cell hidradenocarcinoma is a rare tumor of eccrine sweat gland origin that has a predilection for the head and neck. It has an indolent growth pattern and a higher incidence of regional and distant metastases. Metastasizing adnexal carcinomas are rare; thus, currently there is no uniform treatment guideline. We report a case of an 89-year-old female patient with clear cell hidradenocarcinoma manifesting in the right ear helix that metastasized to the right parotid gland who was treated by wide local excision and radiation therapy.

Using a Triple Helix Approach to Examine Interactions and Dynamics of Innovation in Less-Favoured Regions: The Case of the Portuguese Polytechnic of Guarda

ERIC Educational Resources Information Center

Natário, Manuela; Braga, Ascensão; Daniel, Ana; Rosa, Cecília; Salgado, Miguel

2017-01-01

Using the Triple Helix model, this article examines the contribution of a higher education institution, the Polytechnic of Guarda (PG), located in an inland, a less-favoured region of Portugal, to territorial innovation dynamics. The main goal is to explore how the interaction and cooperation between the three helices of the Guarda region (PG,…

High power, high frequency helix TWT's

NASA Astrophysics Data System (ADS)

Sloley, H. J.; Willard, J.; Paatz, S. R.; Keat, M. J.

The design and performance characteristics of a 34-GHz pulse tube capable of 75 W peak power output at 30 percent duty cycle and a broadband CW tube are presented. Particular attention is given to the engineering problems encountered during the development of the tubes, including the suppression of backward wave oscillation, the design of electron guns for small-diameter high-current beams, and the thermal capability of small helix structures. The discussion also covers the effects of various design parameters and choice of engineering materials on the ultimate practical limit of power and gain at the operating frequencies. Measurements are presented for advanced experimental tubes.

The Effect of a Helix-Coil Transition on the Extension Elasticity

NASA Astrophysics Data System (ADS)

Buhot, Arnaud; Halperin, Avi

2000-03-01

The secondary structure of a polymer affects its deformation behavior in accordance with the Le Chatelier principle. An important example of such secondary structure is the alpha helix encountered in polypeptides. Similar structure was recently proposed for PEO in aqueous media. Our discussion concerns the coupling of the cooperative helix-coil transition and the extension elasticity. In particular, we analyze the extension of a long single chain by use of optical tweezers or AFM. We consider chains that exist in the coil-state when unperturbed. The transition nevertheless occurs because the extension favors the low entropy helical state. As a result, the corresponding force law exhibits a plateau. The analysis of this situation involves two ingredients: (I) the stretching free energy penalty for a rod-coil mutiblock copolymer (II) the entropy associated with the possible placements of the rod and coil blocks.

Structure based aggregation studies reveal the presence of helix-rich intermediate during α-Synuclein aggregation

PubMed Central

Ghosh, Dhiman; Singh, Pradeep K.; Sahay, Shruti; Jha, Narendra Nath; Jacob, Reeba S.; Sen, Shamik; Kumar, Ashutosh; Riek, Roland; Maji, Samir K.

2015-01-01

Mechanistic understanding of nucleation dependent polymerization by α-synuclein (α-Syn) into toxic oligomers and amyloids is important for the drug development against Parkinson's disease. However the structural and morphological characterization during nucleation and subsequent fibrillation process of α-Syn is not clearly understood. Using a variety of complementary biophysical techniques monitoring entire pathway of nine different synucleins, we found that transition of unstructured conformation into β-sheet rich fibril formation involves helix-rich intermediates. These intermediates are common for all aggregating synucleins, contain high solvent-exposed hydrophobic surfaces, are cytotoxic to SHSY-5Y cells and accelerate α-Syn aggregation efficiently. A multidimensional NMR study characterizing the intermediate accompanied with site-specific fluorescence study suggests that the N-terminal and central portions mainly participate in the helix-rich intermediate formation while the C-terminus remained in an extended conformation. However, significant conformational transitions occur at the middle and at the C-terminus during helix to β-sheet transition as evident from Trp fluorescence study. Since partial helix-rich intermediates were also observed for other amyloidogenic proteins such as Aβ and IAPP, we hypothesize that this class of intermediates may be one of the important intermediates for amyloid formation pathway by many natively unstructured protein/peptides and represent a potential target for drug development against amyloid diseases. PMID:25784353

A Helix-Stabilizing Linker Improves Subcutaneous Bioavailability of a Helical Peptide Independent of Linker Lipophilicity

PubMed Central

Zhang, Liang; Navaratna, Tejas; Thurber, Greg M.

2016-01-01

Stabilized peptides address several limitations to peptide-based imaging agents and therapeutics such as poor stability and low affinity due to conformational flexibility. There is also active research in developing these compounds for intracellular drug targeting, and significant efforts have been invested to determine the effects of helix stabilization on intracellular delivery. However, much less is known about the impact on other pharmacokinetic parameters such as plasma clearance and bioavailability. We investigated the effect of different fluorescent helix-stabilizing linkers with varying lipophilicity on subcutaneous (SC) bioavailability using the glucagon-like peptide-1 (GLP-1) receptor ligand exendin as a model system. The stabilized peptides showed significantly higher protease resistance and increased bioavailability independent of linker hydrophilicity, and all subcutaneously delivered conjugates were able to successfully target the islets of Langerhans with high specificity. The lipophilic peptide variants had slower absorption and plasma clearance than their respective hydrophilic conjugates, and the absolute bioavailability was also lower likely due to the longer residence times in the skin. The ease and efficiency of double-click helix stabilization chemistries is a useful tool for increasing the bioavailability of peptide therapeutics, many of which suffer from rapid in vivo protease degradation. Helix stabilization using linkers of varying lipophilicity can further control SC absorption and clearance rates to customize plasma pharmacokinetics. PMID:27327034

A sequential quadratic programming algorithm using an incomplete solution of the subproblem

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murray, W.; Prieto, F.J.

1993-05-01

We analyze sequential quadratic programming (SQP) methods to solve nonlinear constrained optimization problems that are more flexible in their definition than standard SQP methods. The type of flexibility introduced is motivated by the necessity to deviate from the standard approach when solving large problems. Specifically we no longer require a minimizer of the QP subproblem to be determined or particular Lagrange multiplier estimates to be used. Our main focus is on an SQP algorithm that uses a particular augmented Lagrangian merit function. New results are derived for this algorithm under weaker conditions than previously assumed; in particular, it is notmore » assumed that the iterates lie on a compact set.« less

The human early-life exposome (HELIX): project rationale and design.

PubMed

Vrijheid, Martine; Slama, Rémy; Robinson, Oliver; Chatzi, Leda; Coen, Muireann; van den Hazel, Peter; Thomsen, Cathrine; Wright, John; Athersuch, Toby J; Avellana, Narcis; Basagaña, Xavier; Brochot, Celine; Bucchini, Luca; Bustamante, Mariona; Carracedo, Angel; Casas, Maribel; Estivill, Xavier; Fairley, Lesley; van Gent, Diana; Gonzalez, Juan R; Granum, Berit; Gražulevičienė, Regina; Gutzkow, Kristine B; Julvez, Jordi; Keun, Hector C; Kogevinas, Manolis; McEachan, Rosemary R C; Meltzer, Helle Margrete; Sabidó, Eduard; Schwarze, Per E; Siroux, Valérie; Sunyer, Jordi; Want, Elizabeth J; Zeman, Florence; Nieuwenhuijsen, Mark J

2014-06-01

Developmental periods in early life may be particularly vulnerable to impacts of environmental exposures. Human research on this topic has generally focused on single exposure-health effect relationships. The "exposome" concept encompasses the totality of exposures from conception onward, complementing the genome. The Human Early-Life Exposome (HELIX) project is a new collaborative research project that aims to implement novel exposure assessment and biomarker methods to characterize early-life exposure to multiple environmental factors and associate these with omics biomarkers and child health outcomes, thus characterizing the "early-life exposome." Here we describe the general design of the project. In six existing birth cohort studies in Europe, HELIX will estimate prenatal and postnatal exposure to a broad range of chemical and physical exposures. Exposure models will be developed for the full cohorts totaling 32,000 mother-child pairs, and biomarkers will be measured in a subset of 1,200 mother-child pairs. Nested repeat-sampling panel studies (n = 150) will collect data on biomarker variability, use smartphones to assess mobility and physical activity, and perform personal exposure monitoring. Omics techniques will determine molecular profiles (metabolome, proteome, transcriptome, epigenome) associated with exposures. Statistical methods for multiple exposures will provide exposure-response estimates for fetal and child growth, obesity, neurodevelopment, and respiratory outcomes. A health impact assessment exercise will evaluate risks and benefits of combined exposures. HELIX is one of the first attempts to describe the early-life exposome of European populations and unravel its relation to omics markers and health in childhood. As proof of concept, it will form an important first step toward the life-course exposome.

Right- and left-handed three-helix proteins. I. Experimental and simulation analysis of differences in folding and structure.

PubMed

Glyakina, Anna V; Pereyaslavets, Leonid B; Galzitskaya, Oxana V

2013-09-01

Despite the large number of publications on three-helix protein folding, there is no study devoted to the influence of handedness on the rate of three-helix protein folding. From the experimental studies, we make a conclusion that the left-handed three-helix proteins fold faster than the right-handed ones. What may explain this difference? An important question arising in this paper is whether the modeling of protein folding can catch the difference between the protein folding rates of proteins with similar structures but with different folding mechanisms. To answer this question, the folding of eight three-helix proteins (four right-handed and four left-handed), which are similar in size, was modeled using the Monte Carlo and dynamic programming methods. The studies allowed us to determine the orders of folding of the secondary-structure elements in these domains and amino acid residues which are important for the folding. The obtained data are in good correlation with each other and with the experimental data. Structural analysis of these proteins demonstrated that the left-handed domains have a lesser number of contacts per residue and a smaller radius of cross section than the right-handed domains. This may be one of the explanations of the observed fact. The same tendency is observed for the large dataset consisting of 332 three-helix proteins (238 right- and 94 left-handed). From our analysis, we found that the left-handed three-helix proteins have some less-dense packing that should result in faster folding for some proteins as compared to the case of right-handed proteins. Copyright © 2013 Wiley Periodicals, Inc.

Finding Optimal Gains In Linear-Quadratic Control Problems

NASA Technical Reports Server (NTRS)

Milman, Mark H.; Scheid, Robert E., Jr.

1990-01-01

Analytical method based on Volterra factorization leads to new approximations for optimal control gains in finite-time linear-quadratic control problem of system having infinite number of dimensions. Circumvents need to analyze and solve Riccati equations and provides more transparent connection between dynamics of system and optimal gain.

Loop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavity.

PubMed

Manjasetty, Babu A; Halavaty, Andrei S; Luan, Chi-Hao; Osipiuk, Jerzy; Mulligan, Rory; Kwon, Keehwan; Anderson, Wayne F; Joachimiak, Andrzej

2016-04-01

Multidrug transcription regulator AcrR from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 belongs to the tetracycline repressor family, one of the largest groups of bacterial transcription factors. The crystal structure of dimeric AcrR was determined and refined to 1.56Å resolution. The tertiary and quaternary structures of AcrR are similar to those of its homologs. The multidrug binding site was identified based on structural alignment with homologous proteins and has a di(hydroxyethyl)ether molecule bound. Residues from helices α4 and α7 shape the entry into this binding site. The structure of AcrR reveals that the extended helical conformation of helix α4 is stabilized by the hydrogen bond between Glu67 (helix α4) and Gln130 (helix α7). Based on the structural comparison with the closest homolog structure, the Escherichia coli AcrR, we propose that this hydrogen bond is responsible for control of the loop-to-helix transition within helix α4. This local conformational switch of helix α4 may be a key step in accessing the multidrug binding site and securing ligands at the binding site. Solution small-molecule binding studies suggest that AcrR binds ligands with their core chemical structure resembling the tetracyclic ring of cholesterol. Copyright © 2016. Published by Elsevier Inc.

Ligatoxin B, a new cytotoxic protein with a novel helix-turn-helix DNA-binding domain from the mistletoe Phoradendron liga.

PubMed Central

Li, Shi-Sheng; Gullbo, Joachim; Lindholm, Petra; Larsson, Rolf; Thunberg, Eva; Samuelsson, Gunnar; Bohlin, Lars; Claeson, Per

2002-01-01

A new basic protein, designated ligatoxin B, containing 46 amino acid residues has been isolated from the mistletoe Phoradendron liga (Gill.) Eichl. (Viscaceae). The protein's primary structure, determined unambiguously using a combination of automated Edman degradation, trypsin enzymic digestion, and tandem MS analysis, was 1-KSCCPSTTAR-NIYNTCRLTG-ASRSVCASLS-GCKIISGSTC-DSGWNH-46. Ligatoxin B exhibited in vitro cytotoxic activities on the human lymphoma cell line U-937-GTB and the primary multidrug-resistant renal adenocarcinoma cell line ACHN, with IC50 values of 1.8 microM and 3.2 microM respectively. Sequence alignment with other thionins identified a new member of the class 3 thionins, ligatoxin B, which is similar to the earlier described ligatoxin A. As predicted by the method of homology modelling, ligatoxin B shares a three-dimensional structure with the viscotoxins and purothionins and so may have the same mode of cytotoxic action. The novel similarities observed by structural comparison of the helix-turn-helix (HTH) motifs of the thionins, including ligatoxin B, and the HTH DNA-binding proteins, led us to propose the working hypothesis that thionins represent a new group of DNA-binding proteins. This working hypothesis could be useful in further dissecting the molecular mechanisms of thionin cytotoxicity and of thionin opposition to multidrug resistance, and useful in clarifying the physiological function of thionins in plants. PMID:12049612

Genome-wide analysis of basic/helix-loop-helix gene family in peanut and assessment of its roles in pod development.

PubMed

Gao, Chao; Sun, Jianlei; Wang, Chongqi; Dong, Yumei; Xiao, Shouhua; Wang, Xingjun; Jiao, Zigao

2017-01-01

The basic/helix-loop-helix (bHLH) proteins constitute a superfamily of transcription factors that are known to play a range of regulatory roles in eukaryotes. Over the past few decades, many bHLH family genes have been well-characterized in model plants, such as Arabidopsis, rice and tomato. However, the bHLH protein family in peanuts has not yet been systematically identified and characterized. Here, 132 and 129 bHLH proteins were identified from two wild ancestral diploid subgenomes of cultivated tetraploid peanuts, Arachis duranensis (AA) and Arachis ipaensis (BB), respectively. Phylogenetic analysis indicated that these bHLHs could be classified into 19 subfamilies. Distribution mapping results showed that peanut bHLH genes were randomly and unevenly distributed within the 10 AA chromosomes and 10 BB chromosomes. In addition, 120 bHLH gene pairs between the AA-subgenome and BB-subgenome were found to be orthologous and 101 of these pairs were highly syntenic in AA and BB chromosomes. Furthermore, we confirmed that 184 bHLH genes expressed in different tissues, 22 of which exhibited tissue-specific expression. Meanwhile, we identified 61 bHLH genes that may be potentially involved in peanut-specific subterranean. Our comprehensive genomic analysis provides a foundation for future functional dissection and understanding of the regulatory mechanisms of bHLH transcription factors in peanuts.

Ruby-Helix: an implementation of helical image processing based on object-oriented scripting language.

PubMed

Metlagel, Zoltan; Kikkawa, Yayoi S; Kikkawa, Masahide

2007-01-01

Helical image analysis in combination with electron microscopy has been used to study three-dimensional structures of various biological filaments or tubes, such as microtubules, actin filaments, and bacterial flagella. A number of packages have been developed to carry out helical image analysis. Some biological specimens, however, have a symmetry break (seam) in their three-dimensional structure, even though their subunits are mostly arranged in a helical manner. We refer to these objects as "asymmetric helices". All the existing packages are designed for helically symmetric specimens, and do not allow analysis of asymmetric helical objects, such as microtubules with seams. Here, we describe Ruby-Helix, a new set of programs for the analysis of "helical" objects with or without a seam. Ruby-Helix is built on top of the Ruby programming language and is the first implementation of asymmetric helical reconstruction for practical image analysis. It also allows easier and semi-automated analysis, performing iterative unbending and accurate determination of the repeat length. As a result, Ruby-Helix enables us to analyze motor-microtubule complexes with higher throughput to higher resolution.

SclR, a basic helix-loop-helix transcription factor, regulates hyphal morphology and promotes sclerotial formation in Aspergillus oryzae.

PubMed

Jin, Feng Jie; Takahashi, Tadashi; Matsushima, Ken-ichiro; Hara, Seiichi; Shinohara, Yasutomo; Maruyama, Jun-ichi; Kitamoto, Katsuhiko; Koyama, Yasuji

2011-07-01

Most known basic-region helix-loop-helix (bHLH) proteins belong to a superfamily of transcription factors often involved in the control of growth and differentiation. Therefore, inappropriate expression of genes encoding bHLH proteins is frequently associated with developmental dysfunction. In our previously reported study, a novel bHLH protein-encoding gene (AO090011000215) of Aspergillus oryzae was identified. The gene-disrupted strain was found to produce dense conidia, but sparse sclerotia, relative to the parent strain. Here, to further analyze its function, we generated an overexpressing strain using the A. oryzae amyB gene promoter. Genetic overexpression led to a large number of initial hyphal aggregations and then the formation of mature sclerotia; it was therefore designated sclR (sclerotium regulator). At the same time, the sclR-overexpressing strain also displayed both delayed and decreased conidiation. Scanning electron microscopy indicated that the aerial hyphae of the sclR-overexpressing strain were extremely branched and intertwined with each other. In the generation of the SclR-enhanced green fluorescent protein (EGFP) expression strain, the SclR-EGFP protein fusion was conditionally detected in the nuclei. In addition, the loss of sclR function led to rapid protein degradation and cell lysis in dextrin-polypeptone-yeast extract liquid medium. Taken together, these observations indicate that SclR plays an important role in hyphal morphology, asexual conidiospore formation, and the promotion of sclerotial production, even retaining normal cell function, at least in submerged liquid culture.

A Genome-Wide Identification and Analysis of the Basic Helix-Loop-Helix Transcription Factors in Brown Planthopper, Nilaparvata lugens

PubMed Central

Wan, Pin-Jun; Yuan, San-Yue; Wang, Wei-Xia; Chen, Xu; Lai, Feng-Xiang; Fu, Qiang

2016-01-01

The basic helix-loop-helix (bHLH) transcription factors in insects play essential roles in multiple developmental processes including neurogenesis, sterol metabolism, circadian rhythms, organogenesis and formation of olfactory sensory neurons. The identification and function analysis of bHLH family members of the most destructive insect pest of rice, Nilaparvata lugens, may provide novel tools for pest management. Here, a genome-wide survey for bHLH sequences identified 60 bHLH sequences (NlbHLHs) encoded in the draft genome of N. lugens. Phylogenetic analysis of the bHLH domains successfully classified these genes into 40 bHLH families in group A (25), B (14), C (10), D (1), E (8) and F (2). The number of NlbHLHs with introns is higher than many other insect species, and the average intron length is shorter than those of Acyrthosiphon pisum. High number of ortholog families of NlbHLHs was found suggesting functional conversation for these proteins. Compared to other insect species studied, N. lugens has the highest number of bHLH members. Furthermore, gene duplication events of SREBP, Kn(col), Tap, Delilah, Sim, Ato and Crp were found in N. lugens. In addition, a putative full set of NlbHLH genes is defined and compared with another insect species. Thus, our classification of these NlbHLH members provides a platform for further investigations of bHLH protein functions in the regulation of N. lugens, and of insects in general. PMID:27869716

Quadratic constrained mixed discrete optimization with an adiabatic quantum optimizer

NASA Astrophysics Data System (ADS)

Chandra, Rishabh; Jacobson, N. Tobias; Moussa, Jonathan E.; Frankel, Steven H.; Kais, Sabre

2014-07-01

We extend the family of problems that may be implemented on an adiabatic quantum optimizer (AQO). When a quadratic optimization problem has at least one set of discrete controls and the constraints are linear, we call this a quadratic constrained mixed discrete optimization (QCMDO) problem. QCMDO problems are NP-hard, and no efficient classical algorithm for their solution is known. Included in the class of QCMDO problems are combinatorial optimization problems constrained by a linear partial differential equation (PDE) or system of linear PDEs. An essential complication commonly encountered in solving this type of problem is that the linear constraint may introduce many intermediate continuous variables into the optimization while the computational cost grows exponentially with problem size. We resolve this difficulty by developing a constructive mapping from QCMDO to quadratic unconstrained binary optimization (QUBO) such that the size of the QUBO problem depends only on the number of discrete control variables. With a suitable embedding, taking into account the physical constraints of the realizable coupling graph, the resulting QUBO problem can be implemented on an existing AQO. The mapping itself is efficient, scaling cubically with the number of continuous variables in the general case and linearly in the PDE case if an efficient preconditioner is available.

Nonadiabatic rate constants for proton transfer and proton-coupled electron transfer reactions in solution: Effects of quadratic term in the vibronic coupling expansion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soudackov, Alexander V.; Hammes-Schiffer, Sharon

2015-11-21

Rate constant expressions for vibronically nonadiabatic proton transfer and proton-coupled electron transfer reactions are presented and analyzed. The regimes covered include electronically adiabatic and nonadiabatic reactions, as well as high-frequency and low-frequency proton donor-acceptor vibrational modes. These rate constants differ from previous rate constants derived with the cumulant expansion approach in that the logarithmic expansion of the vibronic coupling in terms of the proton donor-acceptor distance includes a quadratic as well as a linear term. The analysis illustrates that inclusion of this quadratic term in the framework of the cumulant expansion framework may significantly impact the rate constants at highmore » temperatures for proton transfer interfaces with soft proton donor-acceptor modes that are associated with small force constants and weak hydrogen bonds. The effects of the quadratic term may also become significant in these regimes when using the vibronic coupling expansion in conjunction with a thermal averaging procedure for calculating the rate constant. In this case, however, the expansion of the coupling can be avoided entirely by calculating the couplings explicitly for the range of proton donor-acceptor distances sampled. The effects of the quadratic term for weak hydrogen-bonding systems are less significant for more physically realistic models that prevent the sampling of unphysical short proton donor-acceptor distances. Additionally, the rigorous relation between the cumulant expansion and thermal averaging approaches is clarified. In particular, the cumulant expansion rate constant includes effects from dynamical interference between the proton donor-acceptor and solvent motions and becomes equivalent to the thermally averaged rate constant when these dynamical effects are neglected. This analysis identifies the regimes in which each rate constant expression is valid and thus will be important for future applications to

Health and Environment Linked for Information Exchange in Atlanta (HELIX-Atlanta): A Pilot Tracking System

NASA Technical Reports Server (NTRS)

Rickman, Doug; Shire, J.; Qualters, J.; Mitchell, K.; Pollard, S.; Rao, R.; Kajumba, N.; Quattrochi, D.; Estes, M., Jr.; Meyer, P.;

Application of quadratic optimization to supersonic inlet control.

NASA Technical Reports Server (NTRS)

Lehtinen, B.; Zeller, J. R.

1972-01-01

This paper describes the application of linear stochastic optimal control theory to the design of the control system for the air intake, the inlet, of a supersonic air-breathing propulsion system. The controls must maintain a stable inlet shock position in the presence of random airflow disturbances and prevent inlet unstart. Two different linear time invariant controllers are developed. One is designed to minimize a nonquadratic index, the expected frequency of inlet unstart, and the other is designed to minimize the mean square value of inlet shock motion. The quadratic equivalence principle is used to obtain a linear controller that minimizes the nonquadratic index. The two controllers are compared on the basis of unstart prevention, control effort requirements, and frequency response. It is concluded that while controls designed to minimize unstarts are desirable in that the index minimized is physically meaningful, computation time required is longer than for the minimum mean square shock position approach. The simpler minimum mean square shock position solution produced expected unstart frequency values which were not significantly larger than those of the nonquadratic solution.

An optimal consumption and investment problem with quadratic utility and negative wealth constraints.

PubMed

Roh, Kum-Hwan; Kim, Ji Yeoun; Shin, Yong Hyun

2017-01-01

In this paper, we investigate the optimal consumption and portfolio selection problem with negative wealth constraints for an economic agent who has a quadratic utility function of consumption and receives a constant labor income. Due to the property of the quadratic utility function, we separate our problem into two cases and derive the closed-form solutions for each case. We also illustrate some numerical implications of the optimal consumption and portfolio.

Global stability and quadratic Hamiltonian structure in Lotka-Volterra and quasi-polynomial systems

NASA Astrophysics Data System (ADS)

Szederkényi, Gábor; Hangos, Katalin M.

2004-04-01

We show that the global stability of quasi-polynomial (QP) and Lotka-Volterra (LV) systems with the well-known logarithmic Lyapunov function is equivalent to the existence of a local generalized dissipative Hamiltonian description of the LV system with a diagonal quadratic form as a Hamiltonian function. The Hamiltonian function can be calculated and the quadratic dissipativity neighborhood of the origin can be estimated by solving linear matrix inequalities.

Elastic Model Transitions Using Quadratic Inequality Constrained Least Squares

NASA Technical Reports Server (NTRS)

Orr, Jeb S.

2012-01-01

A technique is presented for initializing multiple discrete finite element model (FEM) mode sets for certain types of flight dynamics formulations that rely on superposition of orthogonal modes for modeling the elastic response. Such approaches are commonly used for modeling launch vehicle dynamics, and challenges arise due to the rapidly time-varying nature of the rigid-body and elastic characteristics. By way of an energy argument, a quadratic inequality constrained least squares (LSQI) algorithm is employed to e ect a smooth transition from one set of FEM eigenvectors to another with no requirement that the models be of similar dimension or that the eigenvectors be correlated in any particular way. The physically unrealistic and controversial method of eigenvector interpolation is completely avoided, and the discrete solution approximates that of the continuously varying system. The real-time computational burden is shown to be negligible due to convenient features of the solution method. Simulation results are presented, and applications to staging and other discontinuous mass changes are discussed

Spontaneous helix formation in non-chiral bent-core liquid crystals with fast linear electro-optic effect

NASA Astrophysics Data System (ADS)

Sreenilayam, Sithara P.; Panarin, Yuri P.; Vij, Jagdish K.; Panov, Vitaly P.; Lehmann, Anne; Poppe, Marco; Prehm, Marko; Tschierske, Carsten

2016-05-01

Liquid crystals (LCs) represent one of the foundations of modern communication and photonic technologies. Present display technologies are based mainly on nematic LCs, which suffer from limited response time for use in active colour sequential displays and limited image grey scale. Herein we report the first observation of a spontaneously formed helix in a polar tilted smectic LC phase (SmC phase) of achiral bent-core (BC) molecules with the axis of helix lying parallel to the layer normal and a pitch much shorter than the optical wavelength. This new phase shows fast (~30 μs) grey-scale switching due to the deformation of the helix by the electric field. Even more importantly, defect-free alignment is easily achieved for the first time for a BC mesogen, thus providing potential use in large-scale devices with fast linear and thresholdless electro-optical response.

Communications circuit including a linear quadratic estimator

DOEpatents

Ferguson, Dennis D.

2015-07-07

A circuit includes a linear quadratic estimator (LQE) configured to receive a plurality of measurements a signal. The LQE is configured to weight the measurements based on their respective uncertainties to produce weighted averages. The circuit further includes a controller coupled to the LQE and configured to selectively adjust at least one data link parameter associated with a communication channel in response to receiving the weighted averages.

Quadratically Convergent Method for Simultaneously Approaching the Roots of Polynomial Solutions of a Class of Differential Equations

NASA Astrophysics Data System (ADS)

Recchioni, Maria Cristina

2001-12-01

This paper investigates the application of the method introduced by L. Pasquini (1989) for simultaneously approaching the zeros of polynomial solutions to a class of second-order linear homogeneous ordinary differential equations with polynomial coefficients to a particular case in which these polynomial solutions have zeros symmetrically arranged with respect to the origin. The method is based on a family of nonlinear equations which is associated with a given class of differential equations. The roots of the nonlinear equations are related to the roots of the polynomial solutions of differential equations considered. Newton's method is applied to find the roots of these nonlinear equations. In (Pasquini, 1994) the nonsingularity of the roots of these nonlinear equations is studied. In this paper, following the lines in (Pasquini, 1994), the nonsingularity of the roots of these nonlinear equations is studied. More favourable results than the ones in (Pasquini, 1994) are proven in the particular case of polynomial solutions with symmetrical zeros. The method is applied to approximate the roots of Hermite-Sobolev type polynomials and Freud polynomials. A lower bound for the smallest positive root of Hermite-Sobolev type polynomials is given via the nonlinear equation. The quadratic convergence of the method is proven. A comparison with a classical method that uses the Jacobi matrices is carried out. We show that the algorithm derived by the proposed method is sometimes preferable to the classical QR type algorithms for computing the eigenvalues of the Jacobi matrices even if these matrices are real and symmetric.

A three-nucleotide helix I is sufficient for full activity of a hammerhead ribozyme: advantages of an asymmetric design.

PubMed Central

Tabler, M; Homann, M; Tzortzakaki, S; Sczakiel, G

1994-01-01

Trans-cleaving hammerhead ribozymes with long target-specific antisense sequences flanking the catalytic domain share some features with conventional antisense RNA and are therefore termed 'catalytic antisense RNAs'. Sequences 5' to the catalytic domain form helix I and sequences 3' to it form helix III when complexed with the target RNA. A catalytic antisense RNA of more than 400 nucleotides, and specific for the human immunodeficiency virus type 1 (HIV-1), was systematically truncated within the arm that constituted originally a helix I of 128 base pairs. The resulting ribozymes formed helices I of 13, 8, 5, 3, 2, 1 and 0 nucleotides, respectively, and a helix III of about 280 nucleotides. When their in vitro cleavage activity was compared with the original catalytic antisense RNA, it was found that a helix I of as little as three nucleotides was sufficient for full endonucleolytic activity. The catalytically active constructs inhibited HIV-1 replication about four-fold more effectively than the inactive ones when tested in human cells. A conventional hammerhead ribozyme having helices of just 8 nucleotides on either side failed to cleave the target RNA in vitro when tested under the conditions for catalytic antisense RNA. Cleavage activity could only be detected after heat-treatment of the ribozyme substrate mixture which indicates that hammerhead ribozymes with short arms do not associate as efficiently to the target RNA as catalytic antisense RNA. The requirement of just a three-nucleotide helix I allows simple PCR-based generation strategies for asymmetric hammerhead ribozymes. Advantages of an asymmetric design will be discussed. Images PMID:7937118

Insight into conformational changes of a single α-helix peptide molecule through stiffness measurements

NASA Astrophysics Data System (ADS)

Kageshima, Masami; Lantz, Mark A.; Jarvis, Suzanne P.; Tokumoto, Hiroshi; Takeda, Seiji; Ptak, Arkadiusz; Nakamura, Chikashi; Miyake, Jun

2001-07-01

Stiffness variations during the conformational change of a single α-helix polylysine peptide molecule were measured in a liquid environment using atomic force microscopy (AFM) with magnetic cantilever modulation. At the initial stage of the stretching process the stiffness decreased due to the breaking of hydrogen bonds and then increased due to the stretching of the helix backbone. These changes were reversible on reversal of the stretching motion. Below p K, the stiffness did not show increase on reversal, indicating that the reforming of hydrogen bonds did not take place. Conformational changes in the molecule were examined via these changes in stiffness.

Exposure of DNA bases induced by the interaction of DNA and calf thymus DNA helix-destabilizing protein.

PubMed Central

Kohwi-Shigematsu, T; Enomoto, T; Yamada, M A; Nakanishi, M; Tsuboi, M

1978-01-01

The reaction of chloroacetaldehyde with adenine bases in DNA to give a fluorescent product was used to study the availability to intermolecular reaction of positions 1 and 6 of adenine in DNA complexes with calf thymus DNA helix-destabilizing protein. No inhibition of this reaction was observed when heat-denatured DNA was complexed with the protein at a protein/DNA weight ratio of 10:1, compared to free DNA. On the contrary, the same reaction was inhibited markedly for denatured DNA in the presence of calf thymus histone HI at protein/DNA weight ratio of 2:1. Furthermore, the exchange rate for hydrogens of amino and imide groups of DNA bases in DNA strands with deuterium in the solvent was totally unaffected upon complexing of DNA with the DNA helix-destabilizing protein as examined by stopped-flow ultraviolet spectroscopy. These results indicate that the DNA helix-destabilizing protein forms a complex with single-stranded DNA, leaving DNA bases uncovered by the protein. The fluorescence intensity of DNA pretreated with chloroacetaldehyde was amplified by nearly 3-fold upon addition of the DNA helix-destabilizing protein. The possibility of "unstacking" of DNA bases induced by the protein is discussed. PMID:216994

Targeting of Drosophila Rhodopsin Requires Helix 8 but Not the Distal C-Terminus

PubMed Central

Kock, Ines; Bulgakova, Natalia A.; Knust, Elisabeth; Sinning, Irmgard; Panneels, Valérie

2009-01-01

Background The fundamental role of the light receptor rhodopsin in visual function and photoreceptor cell development has been widely studied. Proper trafficking of rhodopsin to the photoreceptor membrane is of great importance. In human, mutations in rhodopsin involving its intracellular mislocalization, are the most frequent cause of autosomal dominant Retinitis Pigmentosa, a degenerative retinal pathology characterized by progressive blindness. Drosophila is widely used as an animal model in visual and retinal degeneration research. So far, little is known about the requirements for proper rhodopsin targeting in Drosophila. Methodology/Principal Findings Different truncated fly-rhodopsin Rh1 variants were expressed in the eyes of Drosophila and their localization was analyzed in vivo or by immunofluorescence. A mutant lacking the last 23 amino acids was found to properly localize in the rhabdomeres, the light-sensing organelle of the photoreceptor cells. This constitutes a major difference to trafficking in vertebrates, which involves a conserved QVxPA motif at the very C-terminus. Further truncations of Rh1 indicated that proper localization requires the last amino acid residues of a region called helix 8 following directly the last transmembrane domain. Interestingly, the very C-terminus of invertebrate visual rhodopsins is extremely variable but helix 8 shows conserved amino acid residues that are not conserved in vertebrate homologs. Conclusions/Significance Despite impressive similarities in the folding and photoactivation of vertebrate and invertebrate visual rhodopsins, a striking difference exists between mammalian and fly rhodopsins in their requirements for proper targeting. Most importantly, the distal part of helix 8 plays a central role in invertebrates. Since the last amino acid residues of helix 8 are dispensable for rhodopsin folding and function, we propose that this domain participates in the recognition of targeting factors involved in

Fast parallel DNA-based algorithms for molecular computation: quadratic congruence and factoring integers.

PubMed

Chang, Weng-Long

2012-03-01

Assume that n is a positive integer. If there is an integer such that M (2) ≡ C (mod n), i.e., the congruence has a solution, then C is said to be a quadratic congruence (mod n). If the congruence does not have a solution, then C is said to be a quadratic noncongruence (mod n). The task of solving the problem is central to many important applications, the most obvious being cryptography. In this article, we describe a DNA-based algorithm for solving quadratic congruence and factoring integers. In additional to this novel contribution, we also show the utility of our encoding scheme, and of the algorithm's submodules. We demonstrate how a variety of arithmetic, shifted and comparative operations, namely bitwise and full addition, subtraction, left shifter and comparison perhaps are performed using strands of DNA.

Technical report. The application of probability-generating functions to linear-quadratic radiation survival curves.

PubMed

Kendal, W S

2000-04-01

To illustrate how probability-generating functions (PGFs) can be employed to derive a simple probabilistic model for clonogenic survival after exposure to ionizing irradiation. Both repairable and irreparable radiation damage to DNA were assumed to occur by independent (Poisson) processes, at intensities proportional to the irradiation dose. Also, repairable damage was assumed to be either repaired or further (lethally) injured according to a third (Bernoulli) process, with the probability of lethal conversion being directly proportional to dose. Using the algebra of PGFs, these three processes were combined to yield a composite PGF that described the distribution of lethal DNA lesions in irradiated cells. The composite PGF characterized a Poisson distribution with mean, chiD+betaD2, where D was dose and alpha and beta were radiobiological constants. This distribution yielded the conventional linear-quadratic survival equation. To test the composite model, the derived distribution was used to predict the frequencies of multiple chromosomal aberrations in irradiated human lymphocytes. The predictions agreed well with observation. This probabilistic model was consistent with single-hit mechanisms, but it was not consistent with binary misrepair mechanisms. A stochastic model for radiation survival has been constructed from elementary PGFs that exactly yields the linear-quadratic relationship. This approach can be used to investigate other simple probabilistic survival models.

Dark-bright quadratic solitons with a focusing effective Kerr nonlinearity

NASA Astrophysics Data System (ADS)

Chen, Manna; Ping, Xiaorou; Liang, Guo; Guo, Qi; Lu, Daquan; Hu, Wei

2018-01-01

Dark solitons are traditionally considered to exist in defocusing Kerr nonlinearity media. We investigate dark quadratic solitons with a focusing effective Kerr nonlinearity and a sine-oscillatory nonlocal response. A nonlinear refractive index with a focusing sine-oscillatory response leads to a defocusing effect with a strong degree of nonlocality, which causes the formation of dark solitons. By analyzing the modulational instability, we determine the parameter domain for dark quadratic solitons with a stable background and numerically obtain dark-bright soliton solutions in the form of pairs, which avoid radiative phenomena. Based on a numerical simulation, we find that all dark-bright soliton pairs are unstable after a relatively long propagation distance, and their stabilities are affected by the soliton interval and the degree of nonlocality.

Treatment effects of quad-helix on the eruption pattern of maxillary second molars.

PubMed

Kobayashi, Yoshiki; Shundo, Isao; Endo, Toshiya

2012-07-01

To evaluate the effects of quad-helix treatment on the eruption pattern of maxillary second molars in patients with maxillary incisor crowding. The lateral cephalograms of 40 consecutively treated patients in the early mixed-dentition group (treatment group) were examined in comparison with those of the same number of untreated patients with a similar form of malocclusion (control group). The cephalograms of the treated patients were taken at the start (T0) and at the end (T1) of treatment, and those of the untreated patients were also taken at about the same time as T0 and T1. The mean ages at T0 and T1 in the two groups were about the same. Distal tipping and movement and impeded extrusion of the maxillary first molars were notable in the treatment group compared with the control group. The actual treatment changes with the use of the quad-helix found expression in distal tipping and impeded vertical eruption of maxillary second molars. The more the maxillary first molars were tipped distally and the less the maxillary first molars extruded, the more the vertical eruption of the maxillary second molars was impeded. Quad-helix treatment gives rise to spontaneous distal tipping and impeded vertical eruption of the maxillary second molars.

Directional passability and quadratic steering logic for pyramid-type single gimbal control moment gyros

NASA Astrophysics Data System (ADS)

Yamada, Katsuhiko; Jikuya, Ichiro

2014-09-01

Singularity analysis and the steering logic of pyramid-type single gimbal control moment gyros are studied. First, a new concept of directional passability in a specified direction is introduced to investigate the structure of an elliptic singular surface. The differences between passability and directional passability are discussed in detail and are visualized for 0H, 2H, and 4H singular surfaces. Second, quadratic steering logic (QSL), a new steering logic for passing the singular surface, is investigated. The algorithm is based on the quadratic constrained quadratic optimization problem and is reduced to the Newton method by using Gröbner bases. The proposed steering logic is demonstrated through numerical simulations for both constant torque maneuvering examples and attitude control examples.

Rendezvous of the "Third Kind": Triple Helix Origins and Future Possibilities

ERIC Educational Resources Information Center

Etzkowitz, Henry

2015-01-01

The Triple Helix, representing university-industry-government interactions, was rooted in a 1993 International Workshop on University-Industry Relations at UNAM's Centro Para la Innovacion Technologica in Mexico City. Impelled by Mexican reality, where university-industry interactions and the institutions themselves operated within a governmental…

The Rice Basic Helix-Loop-Helix Transcription Factor TDR INTERACTING PROTEIN2 Is a Central Switch in Early Anther Development[C][W

PubMed Central

Fu, Zhenzhen; Yu, Jing; Cheng, Xiaowei; Zong, Xu; Xu, Jie; Chen, Mingjiao; Li, Zongyun; Zhang, Dabing; Liang, Wanqi

2014-01-01

In male reproductive development in plants, meristemoid precursor cells possessing transient, stem cell–like features undergo cell divisions and differentiation to produce the anther, the male reproductive organ. The anther contains centrally positioned microsporocytes surrounded by four distinct layers of wall: the epidermis, endothecium, middle layer, and tapetum. Here, we report that the rice (Oryza sativa) basic helix-loop-helix (bHLH) protein TDR INTERACTING PROTEIN2 (TIP2) functions as a crucial switch in the meristemoid transition and differentiation during early anther development. The tip2 mutants display undifferentiated inner three anther wall layers and abort tapetal programmed cell death, causing complete male sterility. TIP2 has two paralogs in rice, TDR and EAT1, which are key regulators of tapetal programmed cell death. We revealed that TIP2 acts upstream of TDR and EAT1 and directly regulates the expression of TDR and EAT1. In addition, TIP2 can interact with TDR, indicating a role of TIP2 in later anther development. Our findings suggest that the bHLH proteins TIP2, TDR, and EAT1 play a central role in regulating differentiation, morphogenesis, and degradation of anther somatic cell layers, highlighting the role of paralogous bHLH proteins in regulating distinct steps of plant cell–type determination. PMID:24755456

Local classifier weighting by quadratic programming.

PubMed

Cevikalp, Hakan; Polikar, Robi

2008-10-01

It has been widely accepted that the classification accuracy can be improved by combining outputs of multiple classifiers. However, how to combine multiple classifiers with various (potentially conflicting) decisions is still an open problem. A rich collection of classifier combination procedures -- many of which are heuristic in nature -- have been developed for this goal. In this brief, we describe a dynamic approach to combine classifiers that have expertise in different regions of the input space. To this end, we use local classifier accuracy estimates to weight classifier outputs. Specifically, we estimate local recognition accuracies of classifiers near a query sample by utilizing its nearest neighbors, and then use these estimates to find the best weights of classifiers to label the query. The problem is formulated as a convex quadratic optimization problem, which returns optimal nonnegative classifier weights with respect to the chosen objective function, and the weights ensure that locally most accurate classifiers are weighted more heavily for labeling the query sample. Experimental results on several data sets indicate that the proposed weighting scheme outperforms other popular classifier combination schemes, particularly on problems with complex decision boundaries. Hence, the results indicate that local classification-accuracy-based combination techniques are well suited for decision making when the classifiers are trained by focusing on different regions of the input space.

Nonadiabatic effects in ultracold molecules via anomalous linear and quadratic Zeeman shifts.

PubMed

McGuyer, B H; Osborn, C B; McDonald, M; Reinaudi, G; Skomorowski, W; Moszynski, R; Zelevinsky, T

2013-12-13

Anomalously large linear and quadratic Zeeman shifts are measured for weakly bound ultracold 88Sr2 molecules near the intercombination-line asymptote. Nonadiabatic Coriolis coupling and the nature of long-range molecular potentials explain how this effect arises and scales roughly cubically with the size of the molecule. The linear shifts yield nonadiabatic mixing angles of the molecular states. The quadratic shifts are sensitive to nearby opposite f-parity states and exhibit fourth-order corrections, providing a stringent test of a state-of-the-art ab initio model.

Structural propensities and entropy effects in peptide helix-coil transitions

NASA Astrophysics Data System (ADS)

Chemmama, Ilan E.; Pelea, Adam Colt; Bhandari, Yuba R.; Chapagain, Prem P.; Gerstman, Bernard S.

2012-09-01

The helix-coil transition in peptides is a critical structural transition leading to functioning proteins. Peptide chains have a large number of possible configurations that must be accounted for in statistical mechanical investigations. Using hydrogen bond and local helix propensity interaction terms, we develop a method for obtaining and incorporating the degeneracy factor that allows the exact calculation of the partition function for a peptide as a function of chain length. The partition function is used in calculations for engineered peptide chains of various lengths that allow comparison with a variety of different types of experimentally measured quantities, such as fraction of helicity as a function of both temperature and chain length, heat capacity, and denaturation studies. When experimental sensitivity in helicity measurements is properly accounted for in the calculations, the calculated curves fit well with the experimental curves. We determine values of interaction energies for comparison with known biochemical interactions, as well as quantify the difference in the number of configurations available to an amino acid in a random coil configuration compared to a helical configuration.

Spontaneous helix formation in non-chiral bent-core liquid crystals with fast linear electro-optic effect

PubMed Central

Sreenilayam, Sithara P.; Panarin, Yuri P.; Vij, Jagdish K.; Panov, Vitaly P.; Lehmann, Anne; Poppe, Marco; Prehm, Marko; Tschierske, Carsten

2016-01-01

Liquid crystals (LCs) represent one of the foundations of modern communication and photonic technologies. Present display technologies are based mainly on nematic LCs, which suffer from limited response time for use in active colour sequential displays and limited image grey scale. Herein we report the first observation of a spontaneously formed helix in a polar tilted smectic LC phase (SmC phase) of achiral bent-core (BC) molecules with the axis of helix lying parallel to the layer normal and a pitch much shorter than the optical wavelength. This new phase shows fast (∼30 μs) grey-scale switching due to the deformation of the helix by the electric field. Even more importantly, defect-free alignment is easily achieved for the first time for a BC mesogen, thus providing potential use in large-scale devices with fast linear and thresholdless electro-optical response. PMID:27156514

Confidence set inference with a prior quadratic bound

NASA Technical Reports Server (NTRS)

Backus, George E.

1989-01-01

In the uniqueness part of a geophysical inverse problem, the observer wants to predict all likely values of P unknown numerical properties z=(z sub 1,...,z sub p) of the earth from measurement of D other numerical properties y (sup 0) = (y (sub 1) (sup 0), ..., y (sub D (sup 0)), using full or partial knowledge of the statistical distribution of the random errors in y (sup 0). The data space Y containing y(sup 0) is D-dimensional, so when the model space X is infinite-dimensional the linear uniqueness problem usually is insoluble without prior information about the correct earth model x. If that information is a quadratic bound on x, Bayesian inference (BI) and stochastic inversion (SI) inject spurious structure into x, implied by neither the data nor the quadratic bound. Confidence set inference (CSI) provides an alternative inversion technique free of this objection. Confidence set inference is illustrated in the problem of estimating the geomagnetic field B at the core-mantle boundary (CMB) from components of B measured on or above the earth's surface.

Linear quadratic stochastic control of atomic hydrogen masers.

PubMed

Koppang, P; Leland, R

1999-01-01

Data are given showing the results of using the linear quadratic Gaussian (LQG) technique to steer remote hydrogen masers to Coordinated Universal Time (UTC) as given by the United States Naval Observatory (USNO) via two-way satellite time transfer and the Global Positioning System (GPS). Data also are shown from the results of steering a hydrogen maser to the real-time USNO mean. A general overview of the theory behind the LQG technique also is given. The LQG control is a technique that uses Kalman filtering to estimate time and frequency errors used as input into a control calculation. A discrete frequency steer is calculated by minimizing a quadratic cost function that is dependent on both the time and frequency errors and the control effort. Different penalties, chosen by the designer, are assessed by the controller as the time and frequency errors and control effort vary from zero. With this feature, controllers can be designed to force the time and frequency differences between two standards to zero, either more or less aggressively depending on the application.

Energy Landscape of the Prion Protein Helix 1 Probed by Metadynamics and NMR

PubMed Central

Camilloni, Carlo; Schaal, Daniel; Schweimer, Kristian; Schwarzinger, Stephan; De Simone, Alfonso

2012-01-01

The characterization of the structural dynamics of proteins, including those that present a substantial degree of disorder, is currently a major scientific challenge. These dynamics are biologically relevant and govern the majority of functional and pathological processes. We exploited a combination of enhanced molecular simulations of metadynamics and NMR measurements to study heterogeneous states of proteins and peptides. In this way, we determined the structural ensemble and free-energy landscape of the highly dynamic helix 1 of the prion protein (PrP-H1), whose misfolding and aggregation are intimately connected to a group of neurodegenerative disorders known as transmissible spongiform encephalopathies. Our combined approach allowed us to dissect the factors that govern the conformational states of PrP-H1 in solution, and the implications of these factors for prion protein misfolding and aggregation. The results underline the importance of adopting novel integrated approaches that take advantage of experiments and theory to achieve a comprehensive characterization of the structure and dynamics of biological macromolecules. PMID:22225810

Use of 1–4 interaction scaling factors to control the conformational equilibrium between α-helix and β-strand

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pang, Yuan-Ping, E-mail: pang@mayo.edu

Highlights: • 1–4 interaction scaling factors are used to adjust conformational energy. • This article reports the effects of these factors on protein conformations. • Reducing these factors changes a helix to a strand in molecular dynamics simulation. • Increasing these factors causes the reverse conformational change. • These factors control the conformational equilibrium between helix and strand. - Abstract: 1–4 interaction scaling factors are used in AMBER forcefields to reduce the exaggeration of short-range repulsion caused by the 6–12 Lennard-Jones potential and a nonpolarizable charge model and to obtain better agreements of small-molecule conformational energies with experimental data. However,more » the effects of these scaling factors on protein secondary structure conformations have not been investigated until now. This article reports the finding that the 1–4 interactions among the protein backbone atoms separated by three consecutive covalent bonds are more repulsive in the α-helix conformation than in two β-strand conformations. Therefore, the 1–4 interaction scaling factors of protein backbone torsions ϕ and ψ control the conformational equilibrium between α-helix and β-strand. Molecular dynamics simulations confirm that reducing the ϕ and ψ scaling factors readily converts the α-helix conformation of AcO-(AAQAA){sub 3}-NH{sub 2} to a β-strand conformation, and the reverse occurs when these scaling factors are increased. These results suggest that the ϕ and ψ scaling factors can be used to generate the α-helix or β-strand conformation in situ and to control the propensities of a forcefield for adopting secondary structure elements.« less

Single-photon transport through a waveguide coupling to a quadratic optomechanical system

NASA Astrophysics Data System (ADS)

Qiao, Lei

2017-07-01

We study the coherent transport of a single photon, which propagates in a one-dimensional waveguide and is scattered by a quadratic optomechanical system. Our approach, which is based on the Lippmann-Schwinger equation, gives an analytical solution to describe the single-photon transmission and reflection properties. We analyze the transport spectra and find they are not only related to the optomechanical system's energy-level structure, but also dependent on the optomechanical system's inherent parameters. For the existence of atomic degrees of freedom, we get a Rabi-splitting-like or an electromagnetically induced transparency (EIT)-like spectrum, depending on the atom-cavity coupling strength. Here, we focus on the single-photon strong-coupling regime so that single-quantum effects could be seen.

Genome-wide identification, classification, and functional analysis of the basic helix-loop-helix transcription factors in the cattle, Bos Taurus.

PubMed

Li, Fengmei; Liu, Wuyi

2017-06-01

The basic helix-loop-helix (bHLH) transcription factors (TFs) form a huge superfamily and play crucial roles in many essential developmental, genetic, and physiological-biochemical processes of eukaryotes. In total, 109 putative bHLH TFs were identified and categorized successfully in the genomic databases of cattle, Bos Taurus, after removing redundant sequences and merging genetic isoforms. Through phylogenetic analyses, 105 proteins among these bHLH TFs were classified into 44 families with 46, 25, 14, 3, 13, and 4 members in the high-order groups A, B, C, D, E, and F, respectively. The remaining 4 bHLH proteins were sorted out as 'orphans.' Next, these 109 putative bHLH proteins identified were further characterized as significantly enriched in 524 significant Gene Ontology (GO) annotations (corrected P value ≤ 0.05) and 21 significantly enriched pathways (corrected P value ≤ 0.05) that had been mapped by the web server KOBAS 2.0. Furthermore, 95 bHLH proteins were further screened and analyzed together with two uncharacterized proteins in the STRING online database to reconstruct the protein-protein interaction network of cattle bHLH TFs. Ultimately, 89 bHLH proteins were fully mapped in a network with 67 biological process, 13 molecular functions, 5 KEGG pathways, 12 PFAM protein domains, and 25 INTERPRO classified protein domains and features. These results provide much useful information and a good reference for further functional investigations and updated researches on cattle bHLH TFs.

Temperature-Triggered Switchable Helix-Helix Inversion of Poly(phenylacetylene) Bearing l-Valine Ethyl Ester Pendants and Its Chiral Recognition Ability.

PubMed

Zhou, Yanli; Zhang, Chunhong; Qiu, Yuan; Liu, Lijia; Yang, Taotao; Dong, Hongxing; Satoh, Toshifumi; Okamoto, Yoshio

2016-11-21

A phenylacetylene containing the l-valine ethyl ester pendant (PAA-Val) was synthesized and polymerized by an organorhodium catalyst (Rh(nbd)BPh₄) to produce the corresponding one-handed helical cis -poly(phenylacetylene) (PPAA-Val). PPAA-Val showed a unique temperature-triggered switchable helix-sense in chloroform, while it was not observed in highly polar solvents, such as N , N '-dimethylformamide (DMF). By heating the solution of PPAA-Val in chloroform, the sign of the CD absorption became reversed, but recovered after cooling the solution to room temperature. Even after six cycles of the heating-cooling treatment, the helix sense of the PPAA-Val's backbone was still switchable without loss of the CD intensity. The PPAA-Val was then coated on silica gel particles to produce novel chiral stationary phases (CSPs) for high-performance liquid chromatography (HPLC). These novel PPAA-Val based CSPs showed a high chiral recognition ability for racemic mandelonitrile ( α = 2.18) and racemic trans - N , N '-diphenylcyclohexane-1,2-dicarboxamide ( α = 2.60). Additionally, the one-handed helical cis -polyene backbone of PPAA-Val was irreversibly destroyed to afford PPAA-Val-H by heating in dimethyl sulfoxide (DMSO) accompanied by the complete disappearance of the Cotton effect. Although PPAA-Val-H had the same l-valine ethyl ester pendants as its cis -isomer PPAA-Val, it showed no chiral recognition. It was concluded that the one-handed helical cis -polyene backbone of PPAA-Val plays an important role in the chiral recognition ability.

Fast Spatial Resolution Analysis of Quadratic Penalized Least-Squares Image Reconstruction With Separate Real and Imaginary Roughness Penalty: Application to fMRI.

PubMed

Olafsson, Valur T; Noll, Douglas C; Fessler, Jeffrey A

2018-02-01

Penalized least-squares iterative image reconstruction algorithms used for spatial resolution-limited imaging, such as functional magnetic resonance imaging (fMRI), commonly use a quadratic roughness penalty to regularize the reconstructed images. When used for complex-valued images, the conventional roughness penalty regularizes the real and imaginary parts equally. However, these imaging methods sometimes benefit from separate penalties for each part. The spatial smoothness from the roughness penalty on the reconstructed image is dictated by the regularization parameter(s). One method to set the parameter to a desired smoothness level is to evaluate the full width at half maximum of the reconstruction method's local impulse response. Previous work has shown that when using the conventional quadratic roughness penalty, one can approximate the local impulse response using an FFT-based calculation. However, that acceleration method cannot be applied directly for separate real and imaginary regularization. This paper proposes a fast and stable calculation for this case that also uses FFT-based calculations to approximate the local impulse responses of the real and imaginary parts. This approach is demonstrated with a quadratic image reconstruction of fMRI data that uses separate roughness penalties for the real and imaginary parts.

Computing the Partial Fraction Decomposition of Rational Functions with Irreducible Quadratic Factors in the Denominators

ERIC Educational Resources Information Center

Man, Yiu-Kwong

2012-01-01

In this note, a new method for computing the partial fraction decomposition of rational functions with irreducible quadratic factors in the denominators is presented. This method involves polynomial divisions and substitutions only, without having to solve for the complex roots of the irreducible quadratic polynomial or to solve a system of linear…

Flexoelectro-optic effect and two-beam energy exchange in a hybrid photorefractive cholesteric cell with a short-pitch horizontal helix

NASA Astrophysics Data System (ADS)

Reshetnyak, V. Yu.; Pinkevych, I. P.; Evans, D. R.

2018-06-01

We develop a theoretical model to describe two-beam energy exchange in a hybrid photorefractive cholesteric cell with a short-pitch helix oriented parallel to the cell substrates (so-called uniformly lying helix configuration). Weak and strong light beams incident on the hybrid cell interfere and induce a periodic space-charge field in the photorefractive substrate of the cell, which penetrates into the cholesteric liquid crystal (LC). Due to the flexoelectro-optic effect an interaction of the photorefractive field with the LC flexopolarization causes the spatially periodic modulation of the helix axis in the plane parallel to the cell substrates. Coupling of a weak signal beam with a strong pump beam at the LC permittivity grating, induced by the periodically tilted helix axis, leads to the energy gain of the weak signal beam. Dependence of the signal beam gain coefficient on the parameters of the short-pitch cholesteric LC is studied.

[The world of double helix--"it did not escape our notice"].

PubMed

Gabryelska, Marta M; Barciszewski, Jan

2013-01-01

One of the key questions of biology is the nature and mechanisms of gene function. It has been 60 years since proposing the right-handed model of DNA double helix in 1953. This discovery was honored with Nobel Prize in 1962 and become a breakthrough in knowing and understanding mechanisms of heredity and genetic code. Since that time a great deal of data have been gathered considering functions, structure and DNA application. It became the basis of modern molecular biology, chemical biology and biotechnology. Today we know, that double helix is characterized by its dynamics and plasticity, which depend on its nucleotide sequence. Chromatin structure and DNA mediated charge transport have a crucial role in understanding mechanisms of its damage and repair. Progress in epigenetics allowed to identify new DNA bases, such as 5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxycytosine. Design of new catalytic nucleic acids and the nanotechnology field of DNA origami reveal its application potential.

Conformational Heterogeneity of Bax Helix 9 Dimer for Apoptotic Pore Formation

NASA Astrophysics Data System (ADS)

Liao, Chenyi; Zhang, Zhi; Kale, Justin; Andrews, David W.; Lin, Jialing; Li, Jianing

2016-07-01

Helix α9 of Bax protein can dimerize in the mitochondrial outer membrane (MOM) and lead to apoptotic pores. However, it remains unclear how different conformations of the dimer contribute to the pore formation on the molecular level. Thus we have investigated various conformational states of the α9 dimer in a MOM model — using computer simulations supplemented with site-specific mutagenesis and crosslinking of the α9 helices. Our data not only confirmed the critical membrane environment for the α9 stability and dimerization, but also revealed the distinct lipid-binding preference of the dimer in different conformational states. In our proposed pathway, a crucial iso-parallel dimer that mediates the conformational transition was discovered computationally and validated experimentally. The corroborating evidence from simulations and experiments suggests that, helix α9 assists Bax activation via the dimer heterogeneity and interactions with specific MOM lipids, which eventually facilitate proteolipidic pore formation in apoptosis regulation.

Engineering quadratic nonlinear photonic crystals for frequency conversion of lasers

NASA Astrophysics Data System (ADS)

Chen, Baoqin; Hong, Lihong; Hu, Chenyang; Zhang, Chao; Liu, Rongjuan; Li, Zhiyuan

2018-03-01

Nonlinear frequency conversion offers an effective way to extend the laser wavelength range. Quadratic nonlinear photonic crystals (NPCs) are artificial materials composed of domain-inversion structures whose sign of nonlinear coefficients are modulated with desire to implement quasi-phase matching (QPM) required for nonlinear frequency conversion. These structures can offer various reciprocal lattice vectors (RLVs) to compensate the phase-mismatching during the quadratic nonlinear optical processes, including second-harmonic generation (SHG), sum-frequency generation and the cascaded third-harmonic generation (THG). The modulation pattern of the nonlinear coefficients is flexible, which can be one-dimensional or two-dimensional (2D), be periodic, quasi-periodic, aperiodic, chirped, or super-periodic. As a result, these NPCs offer very flexible QPM scheme to satisfy various nonlinear optics and laser frequency conversion problems via design of the modulation patterns and RLV spectra. In particular, we introduce the electric poling technique for fabricating QPM structures, a simple effective nonlinear coefficient model for efficiently and precisely evaluating the performance of QPM structures, the concept of super-QPM and super-periodically poled lithium niobate for finely tuning nonlinear optical interactions, the design of 2D ellipse QPM NPC structures enabling continuous tunability of SHG in a broad bandwidth by simply changing the transport direction of pump light, and chirped QPM structures that exhibit broadband RLVs and allow for simultaneous radiation of broadband SHG, THG, HHG and thus coherent white laser from a single crystal. All these technical, theoretical, and physical studies on QPM NPCs can help to gain a deeper insight on the mechanisms, approaches, and routes for flexibly controlling the interaction of lasers with various QPM NPCs for high-efficiency frequency conversion and creation of novel lasers.

Unfolding four-helix bundles

NASA Astrophysics Data System (ADS)

Gray, Harry B.; Winkler, Jay R.; Kozak, John J.

2011-03-01

A geometrical model has been developed to describe the early stages of unfolding of cytochromes c‧ and c-b562 . Calculations are based on a step-wise extension of the polypeptide chain subject to the constraint that the spatial relationship among the residues of each triplet is fixed by the native-state crystallographic data. The response of each protein to these structural perturbations allows the evolution of each of the four helices in these two proteins to be differentiated. It is found that the two external helices in c‧ unfold before its two internal helices, whereas exactly the opposite behaviour is demonstrated by c-b562 . Each of these cytochromes has an extended, internal, non-helical ('turning') region that initially lags behind the most labile helix but then, at a certain stage (identified for each cytochrome), unravels before any of the four helices present in the native structure. It is believed that these predictions will be useful in guiding future experimental studies on the unfolding of these two cytochromes.

The Basic/Helix-Loop-Helix Protein Family in Gossypium: Reference Genes and Their Evolution during Tetraploidization

PubMed Central

Yan, Qian; Liu, Hou-Sheng; Yao, Dan; Li, Xin; Chen, Han; Dou, Yang; Wang, Yi; Pei, Yan; Xiao, Yue-Hua

2015-01-01

Basic/helix-loop-helix (bHLH) proteins comprise one of the largest transcription factor families and play important roles in diverse cellular and molecular processes. Comprehensive analyses of the composition and evolution of the bHLH family in cotton are essential to elucidate their functions and the molecular basis of cotton development. By searching bHLH homologous genes in sequenced diploid cotton genomes (Gossypium raimondii and G. arboreum), a set of cotton bHLH reference genes containing 289 paralogs were identified and named as GobHLH001-289. Based on their phylogenetic relationships, these cotton bHLH proteins were clustered into 27 subfamilies. Compared to those in Arabidopsis and cacao, cotton bHLH proteins generally increased in number, but unevenly in different subfamilies. To further uncover evolutionary changes of bHLH genes during tetraploidization of cotton, all genes of S5a and S5b subfamilies in upland cotton and its diploid progenitors were cloned and compared, and their transcript profiles were determined in upland cotton. A total of 10 genes of S5a and S5b subfamilies (doubled from A- and D-genome progenitors) maintained in tetraploid cottons. The major sequence changes in upland cotton included a 15-bp in-frame deletion in GhbHLH130D and a long terminal repeat retrotransposon inserted in GhbHLH062A, which eliminated GhbHLH062A expression in various tissues. The S5a and S5b bHLH genes of A and D genomes (except GobHLH062) showed similar transcription patterns in various tissues including roots, stems, leaves, petals, ovules, and fibers, while the A- and D-genome genes of GobHLH110 and GobHLH130 displayed clearly different transcript profiles during fiber development. In total, this study represented a genome-wide analysis of cotton bHLH family, and revealed significant changes in sequence and expression of these genes in tetraploid cottons, which paved the way for further functional analyses of bHLH genes in the cotton genus. PMID:25992947

The Basic/Helix-Loop-Helix Protein Family in Gossypium: Reference Genes and Their Evolution during Tetraploidization.

PubMed

Yan, Qian; Liu, Hou-Sheng; Yao, Dan; Li, Xin; Chen, Han; Dou, Yang; Wang, Yi; Pei, Yan; Xiao, Yue-Hua

2015-01-01

Basic/helix-loop-helix (bHLH) proteins comprise one of the largest transcription factor families and play important roles in diverse cellular and molecular processes. Comprehensive analyses of the composition and evolution of the bHLH family in cotton are essential to elucidate their functions and the molecular basis of cotton development. By searching bHLH homologous genes in sequenced diploid cotton genomes (Gossypium raimondii and G. arboreum), a set of cotton bHLH reference genes containing 289 paralogs were identified and named as GobHLH001-289. Based on their phylogenetic relationships, these cotton bHLH proteins were clustered into 27 subfamilies. Compared to those in Arabidopsis and cacao, cotton bHLH proteins generally increased in number, but unevenly in different subfamilies. To further uncover evolutionary changes of bHLH genes during tetraploidization of cotton, all genes of S5a and S5b subfamilies in upland cotton and its diploid progenitors were cloned and compared, and their transcript profiles were determined in upland cotton. A total of 10 genes of S5a and S5b subfamilies (doubled from A- and D-genome progenitors) maintained in tetraploid cottons. The major sequence changes in upland cotton included a 15-bp in-frame deletion in GhbHLH130D and a long terminal repeat retrotransposon inserted in GhbHLH062A, which eliminated GhbHLH062A expression in various tissues. The S5a and S5b bHLH genes of A and D genomes (except GobHLH062) showed similar transcription patterns in various tissues including roots, stems, leaves, petals, ovules, and fibers, while the A- and D-genome genes of GobHLH110 and GobHLH130 displayed clearly different transcript profiles during fiber development. In total, this study represented a genome-wide analysis of cotton bHLH family, and revealed significant changes in sequence and expression of these genes in tetraploid cottons, which paved the way for further functional analyses of bHLH genes in the cotton genus.

Locating the fourth helix: Rethinking the role of civil society in developing smart learning cities

NASA Astrophysics Data System (ADS)

Borkowska, Katarzyna; Osborne, Michael

2018-06-01

In the Global North and increasingly in the Global South, smart city technologies are enthusiastically seen as a solution to urban problems and as an alternative to austerity. However, to move beyond a narrow technological focus, it is necessary to explore the degree to which smart initiatives are committed to building socially inclusive innovation with learning at its core. Using the particular case of the Future City Demonstrator Initiative in Glasgow, United Kingdom, the most high-profile initiative of its kind funded by government, the authors of this article assess the extent to which this smart city adopts such an inclusive approach. They use the quadruple helix model (government - academia - industry - civil society) as a starting point and develop an analytic framework composed of four strands: (1) supporting participation of citizens in decision-making; (2) implementing technological innovation which positions citizens as active users; (3) implementing technological innovation to benefit the community; and (4) evaluating technological innovation in the light of the experiences and needs of citizens. Unlike most analyses, the principal focus of this article is on the fourth element of the helix, civil society. The authors argue that Glasgow's rhetoric of smart urbanism, while aspiring to problem-solving, devalues certain principles of human agency. They emphasise that urban change, including the city's desire to become technologically innovative, would more fully facilitate active citizenship, social inclusion and learning opportunities for all if it were underpinned by the broader conceptions and frameworks of learning cities.

Solving the Integral of Quadratic Forms of Covariance Matrices for Applications in Polarimetric Radar Imagery

NASA Astrophysics Data System (ADS)

Marino, Armando; Hajnsek, Irena

2015-04-01

In this work, the solution of quadratic forms with special application to polarimetric and interferometric covariance matrices is investigated. An analytical solution for the integral of a single quadratic form is derived. Additionally, the integral of the Pol-InSAR coherence (expressed as combination of quadratic forms) is investigated. An approximation for such integral is proposed and defined as Trace coherence. Such approximation is tested on real data to verify that the error is acceptable. The trace coherence can be used for tackle problems related to change detection. Moreover, the use of the Trace coherence in model inversion (as for the RVoG three stage inversion) will be investigated in the future.

Regge trajectories for heavy quarkonia from the quadratic form of the spinless Salpeter-type equation

NASA Astrophysics Data System (ADS)

Chen, Jiao-Kai

2018-03-01

In this paper, we present one new form of the Regge trajectories for heavy quarkonia which is obtained from the quadratic form of the spinless Salpeter-type equation (QSSE) by employing the Bohr-Sommerfeld quantization approach. The obtained Regge trajectories take the parameterized form M^2={β }({c_l}l+{π }n_r+c_0)^{2/3}+c_1, which are different from the present Regge trajectories. Then we apply the obtained Regge trajectories to fit the spectra of charmonia and bottomonia. The fitted Regge trajectories are in good agreement with the experimental data and the theoretical predictions.

Mixing of ultrasonic Lamb waves in thin plates with quadratic nonlinearity.

PubMed

Li, Feilong; Zhao, Youxuan; Cao, Peng; Hu, Ning

2018-07-01

This paper investigates the propagation of Lamb waves in thin plates with quadratic nonlinearity by one-way mixing method using numerical simulations. It is shown that an A 0 -mode wave can be generated by a pair of S 0 and A 0 mode waves only when mixing condition is satisfied, and mixing wave signals are capable of locating the damage zone. Additionally, it is manifested that the acoustic nonlinear parameter increases linearly with quadratic nonlinearity but monotonously with the size of mixing zone. Furthermore, because of frequency deviation, the waveform of the mixing wave changes significantly from a regular diamond shape to toneburst trains. Copyright © 2018 Elsevier B.V. All rights reserved.

Approximating the linear quadratic optimal control law for hereditary systems with delays in the control

NASA Technical Reports Server (NTRS)

Milman, Mark H.

1987-01-01

The fundamental control synthesis issue of establishing a priori convergence rates of approximation schemes for feedback controllers for a class of distributed parameter systems is addressed within the context of hereditary systems. Specifically, a factorization approach is presented for deriving approximations to the optimal feedback gains for the linear regulator-quadratic cost problem associated with time-varying functional differential equations with control delays. The approach is based on a discretization of the state penalty which leads to a simple structure for the feedback control law. General properties of the Volterra factors of Hilbert-Schmidt operators are then used to obtain convergence results for the controls, trajectories and feedback kernels. Two algorithms are derived from the basic approximation scheme, including a fast algorithm, in the time-invariant case. A numerical example is also considered.

Approximating the linear quadratic optimal control law for hereditary systems with delays in the control

NASA Technical Reports Server (NTRS)

Milman, Mark H.

1988-01-01

The fundamental control synthesis issue of establishing a priori convergence rates of approximation schemes for feedback controllers for a class of distributed parameter systems is addressed within the context of hereditary schemes. Specifically, a factorization approach is presented for deriving approximations to the optimal feedback gains for the linear regulator-quadratic cost problem associated with time-varying functional differential equations with control delays. The approach is based on a discretization of the state penalty which leads to a simple structure for the feedback control law. General properties of the Volterra factors of Hilbert-Schmidt operators are then used to obtain convergence results for the controls, trajectories and feedback kernels. Two algorithms are derived from the basic approximation scheme, including a fast algorithm, in the time-invariant case. A numerical example is also considered.

Design of linear quadratic regulators with eigenvalue placement in a specified region

NASA Technical Reports Server (NTRS)

Shieh, Leang-San; Zhen, Liu; Coleman, Norman P.

1990-01-01

Two linear quadratic regulators are developed for placing the closed-loop poles of linear multivariable continuous-time systems within the common region of an open sector, bounded by lines inclined at +/- pi/2k (for a specified integer k not less than 1) from the negative real axis, and the left-hand side of a line parallel to the imaginary axis in the complex s-plane, and simultaneously minimizing a quadratic performance index. The design procedure mainly involves the solution of either Liapunov equations or Riccati equations. The general expression for finding the lower bound of a constant gain gamma is also developed.

Helix-helix inversion of an optically-inactive π-conjugated foldamer triggered by concentration changes of a single enantiomeric guest leading to a change in the helical stability.

PubMed

Liu, Lijia; Ousaka, Naoki; Horie, Miki; Mamiya, Fumihiko; Yashima, Eiji

2016-09-27

A preferred-handed helicity induced in an optically-inactive poly(phenyleneethynylene)-based foldamer bearing carboxylic acid pendants upon complexation with a single enantiomeric diamine was subsequently inverted into the opposite helix upon further addition of the diamine, accompanied by a remarkable change in the stability of the helices.

Analysis of Quadratic Diophantine Equations with Fibonacci Number Solutions

ERIC Educational Resources Information Center

Leyendekkers, J. V.; Shannon, A. G.

2004-01-01

An analysis is made of the role of Fibonacci numbers in some quadratic Diophantine equations. A general solution is obtained for finding factors in sums of Fibonacci numbers. Interpretation of the results is facilitated by the use of a modular ring which also permits extension of the analysis.

Bacterial morphogenesis and the enigmatic MreB helix.

PubMed

Errington, Jeff

2015-04-01

Work over the past decade has highlighted the pivotal role of the actin-like MreB family of proteins in the determination and maintenance of rod cell shape in bacteria. Early images of MreB localization revealed long helical filaments, which were suggestive of a direct role in governing cell wall architecture. However, several more recent, higher-resolution studies have questioned the existence or importance of the helical structures. In this Opinion article, I navigate a path through these conflicting reports, revive the helix model and summarize the key questions that remain to be answered.

Aromatic–aromatic interactions between residues in KCa3.1 pore helix and S5 transmembrane segment control the channel gating process

PubMed Central

Garneau, Line; Klein, Hélène; Lavoie, Marie-France; Brochiero, Emmanuelle; Parent, Lucie

2014-01-01

The Ca2+-activated potassium channel KCa3.1 is emerging as a therapeutic target for a large variety of health disorders. One distinguishing feature of KCa3.1 is that the channel open probability at saturating Ca2+ concentrations (Pomax) is low, typically 0.1–0.2 for KCa3.1 wild type. This observation argues for the binding of Ca2+ to the calmodulin (CaM)–KCa3.1 complex, promoting the formation of a preopen closed-state configuration leading to channel opening. We have previously shown that the KCa3.1 active gate is most likely located at the level of the selectivity filter. As Ca2+-dependent gating of KCa3.1 originates from the binding of Ca2+ to CaM in the C terminus, the hypothesis of a gate located at the level of the selectivity filter requires that the conformational change initiated in the C terminus be transmitted to the S5 and S6 transmembrane helices, with a resulting effect on the channel pore helix directly connected to the selectivity filter. A study was thus undertaken to determine to what extent the interactions between the channel pore helix with the S5 and S6 transmembrane segments contribute to KCa3.1 gating. Molecular dynamics simulations first revealed that the largest contact area between the pore helix and the S5 plus S6 transmembrane helices involves residue F248 at the C-terminal end of the pore helix. Unitary current recordings next confirmed that modulating aromatic–aromatic interactions between F248 and W216 of the S5 transmembrane helical segment and/or perturbing the interactions between F248 and residues in S6 surrounding the glycine hinge G274 cause important changes in Pomax. This work thus provides the first evidence for a key contribution of the pore helix in setting Pomax by stabilizing the channel closed configuration through aromatic–aromatic interactions involving F248 of the pore helix. We propose that the interface pore helix/S5 constitutes a promising site for designing KCa3.1 potentiators. PMID:24470490

The cold-induced basic helix-loop-helix transcription factor gene MdCIbHLH1 encodes an ICE-like protein in apple

PubMed Central

2012-01-01

Background Plant growth is greatly affected by low temperatures, and the expression of a number of genes is induced by cold stress. Although many genes in the cold signaling pathway have been identified in Arabidopsis, little is known about the transcription factors involved in the cold stress response in apple. Results Here, we show that the apple bHLH (basic helix-loop-helix) gene MdCIbHLH1 (Cold-Induced bHLH1), which encodes an ICE-like protein, was noticeably induced in response to cold stress. The MdCIbHLH1 protein specifically bound to the MYC recognition sequences in the AtCBF3 promoter, and MdCIbHLH1 overexpression enhanced cold tolerance in transgenic Arabidopsis. In addition, the MdCIbHLH1 protein bound to the promoters of MdCBF2 and favorably contributed to cold tolerance in transgenic apple plants by upregulating the expression of MdCBF2 through the CBF (C-repeat-binding factor) pathway. Our findings indicate that MdCIbHLH1 functions in stress tolerance in different species. For example, ectopic MdCIbHLH1 expression conferred enhanced chilling tolerance in transgenic tobacco. Finally, we observed that cold induces the degradation of the MdCIbHLH1 protein in apple and that this degradation was potentially mediated by ubiquitination and sumoylation. Conclusions Based on these findings, MdCIbHLH1 encodes a transcription factor that is important for the cold tolerance response in apple. PMID:22336381

Identification of basic/helix-loop-helix transcription factors reveals candidate genes involved in anthocyanin biosynthesis from the strawberry white-flesh mutant.

PubMed

Zhao, Fengli; Li, Gang; Hu, Panpan; Zhao, Xia; Li, Liangjie; Wei, Wei; Feng, Jiayue; Zhou, Houcheng

2018-02-09

As the second largest transcription factor family in plant, the basic helix-loop-helix (bHLH) transcription factor family, characterized by the conserved bHLH domain, plays a central regulatory role in many biological process. However, the bHLH transcription factor family of strawberry has not been systematically identified, especially for the anthocyanin biosynthesis. Here, we identified a total of 113 bHLH transcription factors and described their chromosomal distribution and bioinformatics for the diploid woodland strawberry Fragaria vesca. In addition, transcription profiles of 113 orthologous bHLH genes from various tissues were analyzed for the cultivar 'Benihoppe', its white-flesh mutant 'Xiaobai', and the 'Snow Princess' from their fruit development to the ripening, as well as those under either the ABA or Eth treatment. Both the RT-PCR and qRT-PCR results show that seven selected FabHLH genes (FabHLH17, FabHLH25, FabHLH27, FabHLH29, FabHLH40, FabHLH80, FabHLH98) are responsive to the fruit anthocyanin biosynthesis and hormone signaling according to transcript profiles where three color modes are observed for strawberry's fruit skin and flesh. Further, prediction for the protein interaction network reveals that four bHLHs (FabHLH25, FabHLH29, FabHLH80, FabHLH98) are involved in the fruit anthocyanin biosynthesis and hormone signaling transduction. These bioinformatics and expression profiles provide a good basis for a further investigation of strawberry bHLH genes.

Hyers-Ulam stability of a generalized Apollonius type quadratic mapping

NASA Astrophysics Data System (ADS)

Park, Chun-Gil; Rassias, Themistocles M.

2006-10-01

Let X,Y be linear spaces. It is shown that if a mapping satisfies the following functional equation: then the mapping is quadratic. We moreover prove the Hyers-Ulam stability of the functional equation (0.1) in Banach spaces.

Quadratic Expressions by Means of "Summing All the Matchsticks"

ERIC Educational Resources Information Center

Gierdien, M. Faaiz

2012-01-01

This note presents demonstrations of quadratic expressions that come about when particular problems are posed with respect to matchsticks that form regular triangles, squares, pentagons and so on. Usually when such "matchstick" problems are used as ways to foster algebraic thinking, the expressions for the number of matchstick quantities are…

Interaction of anesthetic molecules with α-helix and polyproline II extended helix of long-chain poly-L-lysine

NASA Astrophysics Data System (ADS)

Cieślik-Boczula, Katarzyna; Rospenk, Maria

2018-01-01

The effect of halothane, enflurane, sevoflurane, and isoflurane molecules, as volatile anesthetics, on the α-helices and polyproline II extended helices (PPII) of long-chain poly-L-lysine (PLL) were studied using Fourier-transform infrared and vibrational circular dichroism spectroscopy. Uncharged and charged α-helices, as well as charged extended PPII helices, were subjected to anesthetic actions in solvents with different pD values or methanol to water ratios. A crucial factor responsible for hindering the anesthetic-PLL interactions is shown to be the ionization of amino groups of the PLL side chains. The α-helix to β-sheet transition was triggered only for the uncharged α-helical structures of PLL by the nonpolar anesthetics under study.

A new numerical approach to solve Thomas-Fermi model of an atom using bio-inspired heuristics integrated with sequential quadratic programming.

PubMed

Raja, Muhammad Asif Zahoor; Zameer, Aneela; Khan, Aziz Ullah; Wazwaz, Abdul Majid

2016-01-01

In this study, a novel bio-inspired computing approach is developed to analyze the dynamics of nonlinear singular Thomas-Fermi equation (TFE) arising in potential and charge density models of an atom by exploiting the strength of finite difference scheme (FDS) for discretization and optimization through genetic algorithms (GAs) hybrid with sequential quadratic programming. The FDS procedures are used to transform the TFE differential equations into a system of nonlinear equations. A fitness function is constructed based on the residual error of constituent equations in the mean square sense and is formulated as the minimization problem. Optimization of parameters for the system is carried out with GAs, used as a tool for viable global search integrated with SQP algorithm for rapid refinement of the results. The design scheme is applied to solve TFE for five different scenarios by taking various step sizes and different input intervals. Comparison of the proposed results with the state of the art numerical and analytical solutions reveals that the worth of our scheme in terms of accuracy and convergence. The reliability and effectiveness of the proposed scheme are validated through consistently getting optimal values of statistical performance indices calculated for a sufficiently large number of independent runs to establish its significance.

Sequential Quadratic Programming Algorithms for Optimization

DTIC Science & Technology

1989-08-01

quadratic program- ma ng (SQ(2l ) aIiatain.seenis to be relgarded aIs tie( buest choice for the solution of smiall. dlense problema (see S tour L)toS...For the step along d, note that a < nOing + 3 szH + i3.ninA A a K f~Iz,;nd and from Id1 _< ,,, we must have that for some /3 , np , 11P11 < dn"p. 5.2...Nevertheless, many of these problems are considered hard to solve. Moreover, for some of these problems the assumptions made in Chapter 2 to establish the

The role of α-, 310-, and π-helix in helix→coil transitions

PubMed Central

Armen, Roger; Alonso, Darwin O.V.; Daggett, Valerie

2003-01-01

The conformational equilibrium between 310- and α-helical structure has been studied via high-resolution NMR spectroscopy by Millhauser and coworkers using the MW peptide Ac-AMAAKAWAAKA AAARA-NH2. Their 750-MHz nuclear Overhauser effect spectroscopy (NOESY) spectra were interpreted to reflect appreciable populations of 310-helix throughout the peptide, with the greatest contribution at the N and C termini. The presence of simultaneous αN(i,i + 2) and αN(i,i + 4) NOE cross-peaks was proposed to represent conformational averaging between 310- and α-helical structures. In this study, we describe 25-nsec molecular dynamics simulations of the MW peptide at 298 K, using both an 8 Å and a 10 Å force-shifted nonbonded cutoff. The ensemble averages of both simulations are in reasonable agreement with the experimental helical content from circular dichroism (CD), the 3JHNα coupling constants, and the 57 observed NOEs. Analysis of the structures from both simulations revealed very little formation of contiguous i → i + 3 hydrogen bonds (310-helix); however, there was a large population of bifurcated i → i + 3 and i → i + 4 α-helical hydrogen bonds. In addition, both simulations contained considerable populations of π-helix (i → i + 5 hydrogen bonds). Individual turns formed over residues 1–9, which we predict contribute to the intensities of the experimentally observed αN(i,i + 2) NOEs. Here we show how sampling of both folded and unfolded structures can provide a structural framework for deconvolution of the conformational contributions to experimental ensemble averages. PMID:12761385

A hydrophobic patch surrounding Trp154 in human neuroserpin controls the helix F dynamics with implications in inhibition and aggregation

NASA Astrophysics Data System (ADS)

Ali, Mohammad Farhan; Kaushik, Abhinav; Kapil, Charu; Gupta, Dinesh; Jairajpuri, Mohamad Aman

2017-02-01

Neuroserpin (NS) mediated inhibition of tissue-type plasminogen activator (tPA) is important for brain development, synapse formation and memory. Aberrations in helix F and β-sheet A movement during inhibition can directly lead to epilepsy or dementia. Conserved W154 residue in a hydrophobic patch between helix F and β-sheet A is ideally placed to control their movement during inhibition. Molecular Dynamics (MD) simulation on wild type (WT) NS and its two variants (W154A and W154P) demonstrated partial deformation in helix F and conformational differences in strands 1A and 2A only in W154P. A fluorescence and Circular Dichroism (CD) analysis with purified W154 variants revealed a significant red-shift and an increase in α-helical content in W154P as compared to W154A and WT NS. Kinetics of tPA inhibition showed a decline in association rates (ka) for W154A as compared to WT NS with indication of complex formation. Appearance of cleaved without complex formation in W154P indicates that the variant acts as substrate due to conformational misfolding around helix F. Both the variants however showed increased rate of aggregation as compared to WT NS. The hydrophobic patch identified in this study may have importance in helix F dynamics of NS.

The N–Terminal Tail of hERG Contains an Amphipathic α–Helix That Regulates Channel Deactivation

PubMed Central

Mobli, Mehdi; Ke, Ying; Kuchel, Philip W.; King, Glenn F.; Stock, Daniela; Vandenberg, Jamie I.

2011-01-01

The cytoplasmic N–terminal domain of the human ether–a–go–go related gene (hERG) K+ channel is critical for the slow deactivation kinetics of the channel. However, the mechanism(s) by which the N–terminal domain regulates deactivation remains to be determined. Here we show that the solution NMR structure of the N–terminal 135 residues of hERG contains a previously described Per–Arnt–Sim (PAS) domain (residues 26–135) as well as an amphipathic α–helix (residues 13–23) and an initial unstructured segment (residues 2–9). Deletion of residues 2–25, only the unstructured segment (residues 2–9) or replacement of the α–helix with a flexible linker all result in enhanced rates of deactivation. Thus, both the initial flexible segment and the α–helix are required but neither is sufficient to confer slow deactivation kinetics. Alanine scanning mutagenesis identified R5 and G6 in the initial flexible segment as critical for slow deactivation. Alanine mutants in the helical region had less dramatic phenotypes. We propose that the PAS domain is bound close to the central core of the channel and that the N–terminal α–helix ensures that the flexible tail is correctly orientated for interaction with the activation gating machinery to stabilize the open state of the channel. PMID:21249148

Optomechanically induced opacity and amplification in a quadratically coupled optomechanical system

NASA Astrophysics Data System (ADS)

Si, Liu-Gang; Xiong, Hao; Zubairy, M. Suhail; Wu, Ying

2017-03-01

We analyze theoretically the features of the output field of a quadratically coupled optomechanical system, which is driven by a strong coupling field and a weak signal field, and in which the membrane (treated as a mechanical resonator) is excited by a weak coherent driving field with two-phonon resonance. We show that the system exhibits complex quantum coherent and interference effects resulting in transmission of the signal field from opacity to remarkable amplification. We also find that the total phase of the applied fields can significantly adjust the signal field's transmission spectrum. The study of the propagation of the signal field in such a quadratically coupled optomechanical system proves that the proposed device can operate as an optical transistor.

Contractions and deformations of quasiclassical Lie algebras preserving a nondegenerate quadratic Casimir operator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Campoamor-Stursberg, R., E-mail: rutwig@mat.ucm.e

2008-05-15

By means of contractions of Lie algebras, we obtain new classes of indecomposable quasiclassical Lie algebras that satisfy the Yang-Baxter equations in its reformulation in terms of triple products. These algebras are shown to arise naturally from noncompact real simple algebras with nonsimple complexification, where we impose that a nondegenerate quadratic Casimir operator is preserved by the limiting process. We further consider the converse problem and obtain sufficient conditions on integrable cocycles of quasiclassical Lie algebras in order to preserve nondegenerate quadratic Casimir operators by the associated linear deformations.

Importance of α–helix N–capping motif in stabilization of ββα fold

PubMed Central

Koscielska-Kasprzak, Katarzyna; Cierpicki, Tomasz; Otlewski, Jacek

2003-01-01

FSD-1 (full sequence design 1) is a protein folded in a ββα motif, designed on the basis of the second zinc finger domain of Zif268 by a substitution of its metal coordination site with a hydrophobic core. In this work, we analyzed the possibility of introducing the DNA recognition motif of the template zinc finger (S13RSDH17) into FSD-1 sequence in order to obtain a small DNA-binding module devoid of cross-link(s) or metal cofactors. The hybrid protein was unfolded, as judged by CD and NMR criteria. To reveal the role of each of the five amino acids, which form the N-capping motif of the α-helix, we analyzed conformational and stability properties of eight FSD-1 mutants. We used a shielded methyl group of Leu 18 and a CD signal at 215 nm as a convenient measure of the folded state. Glu 17→His substitution at the N3 in S13NEKE17 variant decreased the folded structure content from 90% to 25% (equivalent to 1.8 kcal • mole−1 destabilization) by disruption of N-capping interactions, and had the most significant effect among single mutants studied here. The Ncap Asn 14 substitution with Arg considerably decreased stability, reducing structure content from 90% to 40% (1.4 kcal • mole−1 destabilization) by disruption of a helix-capping hydrogen bond and destabilization of a helix macrodipole. The N1 Glu 15→Ser mutation also produced a considerable effect (1.0 kcal • mole−1 destabilization), again emphasizing the significance of electrostatic interactions in α-helix stabilization. PMID:12761399

Antimicrobial Effects of Helix D-derived Peptides of Human Antithrombin III*

PubMed Central

Papareddy, Praveen; Kalle, Martina; Bhongir, Ravi K. V.; Mörgelin, Matthias; Malmsten, Martin; Schmidtchen, Artur

2014-01-01

Antithrombin III (ATIII) is a key antiproteinase involved in blood coagulation. Previous investigations have shown that ATIII is degraded by Staphylococcus aureus V8 protease, leading to release of heparin binding fragments derived from its D helix. As heparin binding and antimicrobial activity of peptides frequently overlap, we here set out to explore possible antibacterial effects of intact and degraded ATIII. In contrast to intact ATIII, the results showed that extensive degradation of the molecule yielded fragments with antimicrobial activity. Correspondingly, the heparin-binding, helix d-derived, peptide FFFAKLNCRLYRKANKSSKLV (FFF21) of human ATIII, was found to be antimicrobial against particularly the Gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa. Fluorescence microscopy and electron microscopy studies demonstrated that FFF21 binds to and permeabilizes bacterial membranes. Analogously, FFF21 was found to induce membrane leakage of model anionic liposomes. In vivo, FFF21 significantly reduced P. aeruginosa infection in mice. Additionally, FFF21 displayed anti-endotoxic effects in vitro. Taken together, our results suggest novel roles for ATIII-derived peptide fragments in host defense. PMID:25202017

Elastic Model Transitions: A Hybrid Approach Utilizing Quadratic Inequality Constrained Least Squares (LSQI) and Direct Shape Mapping (DSM)

NASA Technical Reports Server (NTRS)

Hannan, Mike R.; Jurenko, Robert J.; Bush, Jason; Ottander, John

2014-01-01

A method for transitioning linear time invariant (LTI) models in time varying simulation is proposed that utilizes a hybrid approach for determining physical displacements by augmenting the original quadratically constrained least squares (LSQI) algorithm with Direct Shape Mapping (DSM) and modifying the energy constraints. The approach presented is applicable to simulation of the elastic behavior of launch vehicles and other structures that utilize discrete LTI finite element model (FEM) derived mode sets (eigenvalues and eigenvectors) that are propagated throughout time. The time invariant nature of the elastic data presents a problem of how to properly transition elastic states from the prior to the new model while preserving motion across the transition and ensuring there is no truncation or excitation of the system. A previous approach utilizes a LSQI algorithm with an energy constraint to effect smooth transitions between eigenvector sets with no requirement that the models be of similar dimension or have any correlation. This approach assumes energy is conserved across the transition, which results in significant non-physical transients due to changing quasi-steady state energy between mode sets, a phenomenon seen when utilizing a truncated mode set. The computational burden of simulating a full mode set is significant so a subset of modes is often selected to reduce run time. As a result of this truncation, energy between mode sets may not be constant and solutions across transitions could produce non-physical transients. In an effort to abate these transients an improved methodology was developed based on the aforementioned approach, but this new approach can handle significant changes in energy across mode set transitions. It is proposed that physical velocities due to elastic behavior be solved for using the LSQI algorithm, but solve for displacements using a two-step process that independently addresses the quasi-steady-state and non

Evidence for a central role of PrP helix 2 in the nucleation of amyloid fibrils.

PubMed

Honda, Ryo; Kuwata, Kazuo

2018-02-01

Amyloid fibrils are filamentous protein aggregates associated with the pathogenesis of a wide variety of human diseases. The formation of such aggregates typically follows nucleation-dependent kinetics, wherein the assembly and structural conversion of amyloidogenic proteins into oligomeric aggregates (nuclei) is the rate-limiting step of the overall reaction. In this study, we sought to gain structural insights into the oligomeric nuclei of the human prion protein (PrP) by preparing a series of deletion mutants lacking 14-44 of the C-terminal 107 residues of PrP and examined the kinetics and thermodynamics of these mutants in amyloid formation. An analysis of the experimental data using the concepts of the Φ-value analysis indicated that the helix 2 region (residues 168-196) acquires an amyloid-like β-sheet during nucleation, whereas the other regions preserves a relatively disordered structure in the nuclei. This finding suggests that the helix 2 region serves as the nucleation site for the assembly of amyloid fibrils.-Honda, R., Kuwata, K. Evidence for a central role of PrP helix 2 in the nucleation of amyloid fibrils.

Selection of peptides targeting helix 31 of bacterial 16S ribosomal RNA by screening M13 phage-display libraries.

PubMed

Lamichhane, Tek N; Abeydeera, N Dinuka; Duc, Anne-Cécile E; Cunningham, Philip R; Chow, Christine S

2011-01-28

Ribosomal RNA is the catalytic portion of ribosomes, and undergoes a variety of conformational changes during translation. Structural changes in ribosomal RNA can be facilitated by the presence of modified nucleotides. Helix 31 of bacterial 16S ribosomal RNA harbors two modified nucleotides, m²G966 and m⁵C967, that are highly conserved among bacteria, though the degree and nature of the modifications in this region are different in eukaryotes. Contacts between helix 31 and the P-site tRNA, initiation factors, and ribosomal proteins highlight the importance of this region in translation. In this work, a heptapeptide M13 phage-display library was screened for ligands that target the wild-type, naturally modified bacterial helix 31. Several peptides, including TYLPWPA, CVRPFAL, TLWDLIP, FVRPFPL, ATPLWLK, and DIRTQRE, were found to be prevalent after several rounds of screening. Several of the peptides exhibited moderate affinity (in the high nM to low µM range) to modified helix 31 in biophysical assays, including surface plasmon resonance (SPR), and were also shown to bind 30S ribosomal subunits. These peptides also inhibited protein synthesis in cell-free translation assays.

Tip-tilt disturbance model identification based on non-linear least squares fitting for Linear Quadratic Gaussian control

NASA Astrophysics Data System (ADS)

Yang, Kangjian; Yang, Ping; Wang, Shuai; Dong, Lizhi; Xu, Bing

2018-05-01

We propose a method to identify tip-tilt disturbance model for Linear Quadratic Gaussian control. This identification method based on Levenberg-Marquardt method conducts with a little prior information and no auxiliary system and it is convenient to identify the tip-tilt disturbance model on-line for real-time control. This identification method makes it easy that Linear Quadratic Gaussian control runs efficiently in different adaptive optics systems for vibration mitigation. The validity of the Linear Quadratic Gaussian control associated with this tip-tilt disturbance model identification method is verified by experimental data, which is conducted in replay mode by simulation.

Convexity Conditions and the Legendre-Fenchel Transform for the Product of Finitely Many Positive Definite Quadratic Forms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao Yunbin, E-mail: zhaoyy@maths.bham.ac.u

2010-12-15

While the product of finitely many convex functions has been investigated in the field of global optimization, some fundamental issues such as the convexity condition and the Legendre-Fenchel transform for the product function remain unresolved. Focusing on quadratic forms, this paper is aimed at addressing the question: When is the product of finitely many positive definite quadratic forms convex, and what is the Legendre-Fenchel transform for it? First, we show that the convexity of the product is determined intrinsically by the condition number of so-called 'scaled matrices' associated with quadratic forms involved. The main result claims that if the conditionmore » number of these scaled matrices are bounded above by an explicit constant (which depends only on the number of quadratic forms involved), then the product function is convex. Second, we prove that the Legendre-Fenchel transform for the product of positive definite quadratic forms can be expressed, and the computation of the transform amounts to finding the solution to a system of equations (or equally, finding a Brouwer's fixed point of a mapping) with a special structure. Thus, a broader question than the open 'Question 11' in Hiriart-Urruty (SIAM Rev. 49, 225-273, 2007) is addressed in this paper.« less

Quadratic Electro-optic Effect in a Novel Nonconjugated Conductive Polymer, iodine-doped Polynorbornene

NASA Astrophysics Data System (ADS)

Narayanan, Ananthakrishnan; Thakur, Mrinal

2009-03-01

Quadratic electro-optic effect in a novel nonconjugated conductive polymer, iodine-doped polynorbornene has been measured using field-induced birefringence at 633 nm. The electrical conductivity^1 of polynorbornene increases by twelve orders of magnitude to about 0.01 S/cm upon doping with iodine. The electro-optic measurement has been made in a film doped at the medium doping-level. The electro-optic modulation signal was recorded using a lock-in amplifier for various applied ac voltages (4 kHz) and the quadratic dependence of the modulation on the applied voltage was observed. A modulation of about 0.01% was observed for an applied electric field of 3 V/micron for a 100 nm thick film The Kerr coefficient as determined is about 1.77x10-11m/V^2. This exceptionally large quadratic electro-optic effect has been attributed to the confinement of this charge-transfer system within a sub-nanometer dimension. 1. A. Narayanan, A. Palthi and M. Thakur, J. Macromol. Sci. -- PAC, accepted.

A new family of β-helix proteins with similarities to the polysaccharide lyases

DOE PAGES

Close, Devin W.; D'Angelo, Sara; Bradbury, Andrew R. M.

2014-09-27

Microorganisms that degrade biomass produce diverse assortments of carbohydrate-active enzymes and binding modules. Despite tremendous advances in the genomic sequencing of these organisms, many genes do not have an ascribed function owing to low sequence identity to genes that have been annotated. Consequently, biochemical and structural characterization of genes with unknown function is required to complement the rapidly growing pool of genomic sequencing data. A protein with previously unknown function (Cthe_2159) was recently isolated in a genome-wide screen using phage display to identify cellulose-binding protein domains from the biomass-degrading bacterium Clostridium thermocellum. Here, the crystal structure of Cthe_2159 is presentedmore » and it is shown that it is a unique right-handed parallel β-helix protein. Despite very low sequence identity to known β-helix or carbohydrate-active proteins, Cthe_2159 displays structural features that are very similar to those of polysaccharide lyase (PL) families 1, 3, 6 and 9. Cthe_2159 is conserved across bacteria and some archaea and is a member of the domain of unknown function family DUF4353. This suggests that Cthe_2159 is the first representative of a previously unknown family of cellulose and/or acid-sugar binding β-helix proteins that share structural similarities with PLs. More importantly, these results demonstrate how functional annotation by biochemical and structural analysis remains a critical tool in the characterization of new gene products.« less

A new family of β-helix proteins with similarities to the polysaccharide lyases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Close, Devin W.; D'Angelo, Sara; Bradbury, Andrew R. M.

Microorganisms that degrade biomass produce diverse assortments of carbohydrate-active enzymes and binding modules. Despite tremendous advances in the genomic sequencing of these organisms, many genes do not have an ascribed function owing to low sequence identity to genes that have been annotated. Consequently, biochemical and structural characterization of genes with unknown function is required to complement the rapidly growing pool of genomic sequencing data. A protein with previously unknown function (Cthe_2159) was recently isolated in a genome-wide screen using phage display to identify cellulose-binding protein domains from the biomass-degrading bacterium Clostridium thermocellum. Here, the crystal structure of Cthe_2159 is presentedmore » and it is shown that it is a unique right-handed parallel β-helix protein. Despite very low sequence identity to known β-helix or carbohydrate-active proteins, Cthe_2159 displays structural features that are very similar to those of polysaccharide lyase (PL) families 1, 3, 6 and 9. Cthe_2159 is conserved across bacteria and some archaea and is a member of the domain of unknown function family DUF4353. This suggests that Cthe_2159 is the first representative of a previously unknown family of cellulose and/or acid-sugar binding β-helix proteins that share structural similarities with PLs. More importantly, these results demonstrate how functional annotation by biochemical and structural analysis remains a critical tool in the characterization of new gene products.« less

Human telomeric DNA: G-quadruplex, i-motif and Watson–Crick double helix

PubMed Central

Phan, Anh Tuân; Mergny, Jean-Louis

2002-01-01

Human telomeric DNA composed of (TTAGGG/CCCTAA)n repeats may form a classical Watson–Crick double helix. Each individual strand is also prone to quadruplex formation: the G-rich strand may adopt a G-quadruplex conformation involving G-quartets whereas the C-rich strand may fold into an i-motif based on intercalated C·C+ base pairs. Using an equimolar mixture of the telomeric oligonucleotides d[AGGG(TTAGGG)3] and d[(CCCTAA)3CCCT], we defined which structures existed and which would be the predominant species under a variety of experimental conditions. Under near-physiological conditions of pH, temperature and salt concentration, telomeric DNA was predominantly in a double-helix form. However, at lower pH values or higher temperatures, the G-quadruplex and/or the i-motif efficiently competed with the duplex. We also present kinetic and thermodynamic data for duplex association and for G-quadruplex/i-motif unfolding. PMID:12409451

Molecular mechanism of polyacrylate helix sense switching across its free energy landscape.

PubMed

Pietropaolo, Adriana; Nakano, Tamaki

2013-04-17

Helical polymers with switchable screw sense are versatile frameworks for chiral functional materials. In this work, we reconstructed the free energy landscape of helical poly(2,7-bis(4-tert-butylphenyl)fluoren-9-yl acrylate) [poly(BBPFA)], as its racemization is selectively driven by light without any rearrangement of chemical bonds. The chirality inversion was enforced by atomistic free energy simulations using chirality indices as reaction coordinates. The free energy landscape reproduced the experimental electronic circular dichroism spectra. We propose that the chirality inversion of poly(BBPFA) proceeds from a left-handed 31 helix via multistate free energy pathways to reach the right-handed 31 helix. The inversion is triggered by the rotation of biphenyl units with an activation barrier of 38 kcal/mol. To the best of our knowledge, this is the first report on the chiral inversion mechanism of a helical polymer determined in a quantitative way in the framework of atomistic free energy simulations.

Salt bridge interactions within the β2 integrin α7 helix mediate force-induced binding and shear resistance ability.

PubMed

Zhang, Xiao; Li, Linda; Li, Ning; Shu, Xinyu; Zhou, Lüwen; Lü, Shouqin; Chen, Shenbao; Mao, Debin; Long, Mian

2018-01-01

The functional performance of the αI domain α 7 helix in β 2 integrin activation depends on the allostery of the α 7 helix, which axially slides down; therefore, it is critical to elucidate what factors regulate the allostery. In this study, we determined that there were two conservative salt bridge interaction pairs that constrain both the upper and bottom ends of the α 7 helix. Molecular dynamics (MD) simulations for three β 2 integrin members, lymphocyte function-associated antigen-1 (LFA-1; α L β 2 ), macrophage-1 antigen (Mac-1; α M β 2 ) and α x β 2 , indicated that the magnitude of the salt bridge interaction is related to the stability of the αI domain and the strength of the corresponding force-induced allostery. The disruption of the salt bridge interaction, especially with double mutations in both salt bridges, significantly reduced the force-induced allostery time for all three members. The effects of salt bridge interactions of the αI domain α 7 helix on β 2 integrin conformational stability and allostery were experimentally validated using Mac-1 constructs. The results demonstrated that salt bridge mutations did not alter the conformational state of Mac-1, but they did increase the force-induced ligand binding and shear resistance ability, which was consistent with MD simulations. This study offers new insight into the importance of salt bridge interaction constraints of the αI domain α 7 helix and external force for β 2 integrin function. © 2017 Federation of European Biochemical Societies.

DQM: Decentralized Quadratically Approximated Alternating Direction Method of Multipliers

NASA Astrophysics Data System (ADS)

Mokhtari, Aryan; Shi, Wei; Ling, Qing; Ribeiro, Alejandro

2016-10-01

This paper considers decentralized consensus optimization problems where nodes of a network have access to different summands of a global objective function. Nodes cooperate to minimize the global objective by exchanging information with neighbors only. A decentralized version of the alternating directions method of multipliers (DADMM) is a common method for solving this category of problems. DADMM exhibits linear convergence rate to the optimal objective but its implementation requires solving a convex optimization problem at each iteration. This can be computationally costly and may result in large overall convergence times. The decentralized quadratically approximated ADMM algorithm (DQM), which minimizes a quadratic approximation of the objective function that DADMM minimizes at each iteration, is proposed here. The consequent reduction in computational time is shown to have minimal effect on convergence properties. Convergence still proceeds at a linear rate with a guaranteed constant that is asymptotically equivalent to the DADMM linear convergence rate constant. Numerical results demonstrate advantages of DQM relative to DADMM and other alternatives in a logistic regression problem.

Linear-Quadratic-Gaussian Regulator Developed for a Magnetic Bearing

NASA Technical Reports Server (NTRS)

Choi, Benjamin B.

2002-01-01

Linear-Quadratic-Gaussian (LQG) control is a modern state-space technique for designing optimal dynamic regulators. It enables us to trade off regulation performance and control effort, and to take into account process and measurement noise. The Structural Mechanics and Dynamics Branch at the NASA Glenn Research Center has developed an LQG control for a fault-tolerant magnetic bearing suspension rig to optimize system performance and to reduce the sensor and processing noise. The LQG regulator consists of an optimal state-feedback gain and a Kalman state estimator. The first design step is to seek a state-feedback law that minimizes the cost function of regulation performance, which is measured by a quadratic performance criterion with user-specified weighting matrices, and to define the tradeoff between regulation performance and control effort. The next design step is to derive a state estimator using a Kalman filter because the optimal state feedback cannot be implemented without full state measurement. Since the Kalman filter is an optimal estimator when dealing with Gaussian white noise, it minimizes the asymptotic covariance of the estimation error.

The Helix Nebula Viewed in HCO+: Large-scale Mapping of the J = 1 → 0 Transition

NASA Astrophysics Data System (ADS)

Zeigler, N. R.; Zack, L. N.; Woolf, N. J.; Ziurys, L. M.

2013-11-01

The J = 1 → 0 transition of HCO+ at 89 GHz has been mapped across the Helix Nebula (NGC 7293) with 70'' spatial resolution (1.68 km s-1 velocity resolution) using the Arizona Radio Observatory 12 m telescope. This work is the first large-scale mapping project of a dense gas tracer (n(H2) ~ 105 cm-3) in old planetary nebulae. Observations of over 200 positions encompassing the classical optical image were conducted with a 3σ noise level of ~20 mK. HCO+ was detected at most positions, often exhibiting multiple velocity components indicative of complex kinematic structures in dense gas. The HCO+ spectra suggest that the Helix is composed of a bipolar, barrel-like structure with red- and blue-shifted halves, symmetric with respect to the central star and oriented ~10° east from the line of sight. A second bipolar, higher velocity outflow exists as well, situated along the direction of the Helix "plumes." The column density of HCO+ across the Helix is N tot ~ 1.5 × 1010-5.0 × 1011 cm-2, with an average value N ave ~ 1 × 1011 cm-2, corresponding to an abundance, relative to H2, of f ~ 1.4 × 10-8. This value is similar to that observed in young PN, and contradicts chemical models, which predict that the abundance of HCO+ decreases with nebular age. This study indicates that polyatomic molecules readily survive the ultraviolet field of the central white dwarf, and can be useful in tracing nebular morphology in the very late stages of stellar evolution.

Revealing Ozgur's Thoughts of a Quadratic Function with a Clinical Interview: Concepts and Their Underlying Reasons

ERIC Educational Resources Information Center

Ozaltun Celik, Aytug; Bukova Guzel, Esra

2017-01-01

The quadratic function is an important concept for calculus but the students at high school have many difficulties related to this concept. It is important that the teaching of the quadratic function is realized considering the students' thinking. In this context, the aim of this study conducted through a qualitative case study is to reveal the…

Caspase-like activity is essential for long-term synaptic plasticity in the terrestrial snail Helix.

PubMed

Bravarenko, N I; Onufriev, M V; Stepanichev, M Yu; Ierusalimsky, V N; Balaban, P M; Gulyaeva, N V

2006-01-01

Although caspase activity in the nervous system of mollusks has not been described before, we suggested that these cysteine proteases might be involved in the phenomena of neuroplasticity in mollusks. We directly measured caspase-3 (DEVDase) activity in the Helix lucorum central nervous system (CNS) using a fluorometrical approach and showed that the caspase-3-like immunoreactivity is present in the central neurons of Helix. Western blots revealed the presence of caspase-3-immunoreactive proteins with a molecular mass of 29 kDa. Staurosporin application, routinely used to induce apoptosis in mammalian neurons through the activating cleavage of caspase-3, did not result in the appearance of a smaller subunit corresponding to the active caspase in the snail. However, it did increase the enzyme activity in the snail CNS. This suggests differences in the regulation of caspase-3 activity in mammals and snails. In the snail CNS, the caspase homolog seems to possess an active center without activating cleavage typical for mammals. In electrophysiological experiments with identified snail neurons, selective blockade of the caspase-3 with the irreversible and cell-permeable inhibitor of caspase-3 N-benzyloxycarbonyl-Asp(OMe)-Glu(OMe)-Val-Asp-(OMe)-fluoro-methylketone prevented development of the long-term stage of synaptic input sensitization, suggesting that caspase is necessary for normal synaptic plasticity in snails. The results of our study give the first direct evidence that the caspase-3-like activity is essential for long-term plasticity in the invertebrate neurons. This activity is presumably involved in removing inhibitory constraints on the storage of long-term memory.

Symmetry-breaking instability of quadratic soliton bound states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Delque, Michaeel; Departement d'Optique P.M. Duffieux, Institut FEMTO-ST, Universite de Franche-Comte, CNRS UMR 6174, F-25030 Besancon; Fanjoux, Gil

We study both numerically and experimentally two-dimensional soliton bound states in quadratic media and demonstrate their symmetry-breaking instability. The experiment is performed in a potassium titanyl phosphate crystal in a type-II configuration. The bound state is generated by the copropagation of the antisymmetric fundamental beam locked in phase with the symmetrical second harmonic one. Experimental results are in good agreement with numerical simulations of the nonlinear wave equations.

Genomic organization and chromosomal localization of the gene TCF15 encoding the early mesodermal basic helix-loop-helix factor bHLH-EC2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hidai, H.; Quertermous, E.E.; Quertermous, T.

1995-12-10

bHLH-EC2 is a recently characterized member of a growing family of basic helix-loop-helix transcription factors. This family includes bHLH factors such as twist, which appear to be primarily involved in early mesodermal differentiation, and bHLH factors such as TAL-1, which have been characterized through their association with chromosomal breakpoints associated with T-cell leukemias. To provide for studies aimed at understanding the genetic regulation of bHLH-EC2, we have characterized the organization of this gene and conducted preliminary studies of the transcriptional activity of the upstream promoter region. The mouse bHLH-EC2 gene was found to consist of two exons separated by amore » 5-kb intron, an organization pattern similar to the mouse twist gene. The transcription initiation site was identified by RNase protection assay and primer extension analysis. Linked promoter-reporter gene transfection experiments in cultured cells indicated that while the identified upstream sequence can function to promote transcription, it does not function in a cell-specific fashion. To investigate the possible association of bHLH-EC2 with hematological malignancy, the chromosomal location of this gene in the human was mapped by fluorescence in situ hybridization and assigned to chromosome band 20p13. 16 refs., 3 figs.« less

Linear quadratic regulators with eigenvalue placement in a horizontal strip

NASA Technical Reports Server (NTRS)

Shieh, Leang S.; Dib, Hani M.; Ganesan, Sekar

1987-01-01

A method for optimally shifting the imaginary parts of the open-loop poles of a multivariable control system to the desirable closed-loop locations is presented. The optimal solution with respect to a quadratic performance index is obtained by solving a linear matrix Liapunov equation.

Stochastic resonance in a fractional oscillator driven by multiplicative quadratic noise

NASA Astrophysics Data System (ADS)

Ren, Ruibin; Luo, Maokang; Deng, Ke

2017-02-01

Stochastic resonance of a fractional oscillator subject to an external periodic field as well as to multiplicative and additive noise is investigated. The fluctuations of the eigenfrequency are modeled as the quadratic function of the trichotomous noise. Applying the moment equation method and Shapiro-Loginov formula, we obtain the exact expression of the complex susceptibility and related stability criteria. Theoretical analysis and numerical simulations indicate that the spectral amplification (SPA) depends non-monotonicly both on the external driving frequency and the parameters of the quadratic noise. In addition, the investigations into fractional stochastic systems have suggested that both the noise parameters and the memory effect can induce the phenomenon of stochastic multi-resonance (SMR), which is previously reported and believed to be absent in the case of the multiplicative noise with only a linear term.

Thermal response test data of five quadratic cross section precast pile heat exchangers.

PubMed

Alberdi-Pagola, Maria

2018-06-01

This data article comprises records from five Thermal Response Tests (TRT) of quadratic cross section pile heat exchangers. Pile heat exchangers, typically referred to as energy piles, consist of traditional foundation piles with embedded heat exchanger pipes. The data presented in this article are related to the research article entitled "Comparing heat flow models for interpretation of precast quadratic pile heat exchanger thermal response tests" (Alberdi-Pagola et al., 2018) [1]. The TRT data consists of measured inlet and outlet temperatures, fluid flow and injected heat rate recorded every 10 min. The field dataset is made available to enable model verification studies.

Self-repeating properties of four-petal Gaussian vortex beams in quadratic index medium

NASA Astrophysics Data System (ADS)

Zou, Defeng; Li, Xiaohui; Chai, Tong; Zheng, Hairong

2018-05-01

In this paper, we investigate the propagation properties of four-petal Gaussian vortex (FPGV) beams propagating through the quadratic index medium, obtaining the analytical expression of FPGV beams. The effects of beam order n, topological charge m and beam waist ω0 are investigated. Results show that quadratic index medium support periodic distributions of FPGV beams. A hollow optical wall or an optical central principal maximum surrounded by symmetrical sidelobes will occur at the center of a period. At length, they will evolve into four petals structure, exactly same as the intensity distributions at source plane.

Relative Stability of the Scleroglucan Triple-Helix and Single Strand: an Insight from Computational and Experimental Techniques

NASA Astrophysics Data System (ADS)

Bocchinfuso, Gianfranco; Mazzuca, Claudia; Conflitti, Paolo; Cori, Davide; Coviello, Tommasina; Palleschi, Antonio

2016-09-01

Scleroglucan (Sclg) is a polysaccharide that exhibits a triple helix conformation (triplex), both in aqueous solution and in the solid state, which is lost in DMSO solution, at high temperature and at high pH values. The triplex conformation is characterized by a high rigidity, responsible of Sclg peculiar properties. Although the relative stability of triplex and single strand has already been investigated, different structural details are still missing. In the present study, we analyse the structural properties and the factors stabilizing the single chain and the triple helix of Sclg in different conditions. To this end, we simulated both systems in water and in DMSO. The triple helix has been also simulated in the presence of chemical damages on one of the three strands (to reproduce in silico the effect of sonication) or by inducing a partial unfolding of the triplex structure. The computational results have been compared with experimental evidences in which the triplex denaturation, at alkaline pH values, has been followed by monitoring the UV and CD spectra of Congo red, used as a probe molecule. Our results indicate that sonication breaks the Sclg chains without appreciably changing the stability of the other tracts of triple helix. The simulated perturbed or partially unfolded triplexes show a clear tendency to form less ordered aggregates. Finally, our simulations put in evidence an important role of the hydrophobic interactions both in the triplex stability and in the aggregation processes observed after induced denaturation.

A conserved phenylalanine as a relay between the α5 helix and the GDP binding region of heterotrimeric Gi protein α subunit.

PubMed

Kaya, Ali I; Lokits, Alyssa D; Gilbert, James A; Iverson, Tina M; Meiler, Jens; Hamm, Heidi E

2014-08-29

G protein activation by G protein-coupled receptors is one of the critical steps for many cellular signal transduction pathways. Previously, we and other groups reported that the α5 helix in the G protein α subunit plays a major role during this activation process. However, the precise signaling pathway between the α5 helix and the guanosine diphosphate (GDP) binding pocket remains elusive. Here, using structural, biochemical, and computational techniques, we probed different residues around the α5 helix for their role in signaling. Our data showed that perturbing the Phe-336 residue disturbs hydrophobic interactions with the β2-β3 strands and α1 helix, leading to high basal nucleotide exchange. However, mutations in β strands β5 and β6 do not perturb G protein activation. We have highlighted critical residues that leverage Phe-336 as a relay. Conformational changes are transmitted starting from Phe-336 via β2-β3/α1 to Switch I and the phosphate binding loop, decreasing the stability of the GDP binding pocket and triggering nucleotide release. When the α1 and α5 helices were cross-linked, inhibiting the receptor-mediated displacement of the C-terminal α5 helix, mutation of Phe-336 still leads to high basal exchange rates. This suggests that unlike receptor-mediated activation, helix 5 rotation and translocation are not necessary for GDP release from the α subunit. Rather, destabilization of the backdoor region of the Gα subunit is sufficient for triggering the activation process. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Thermodynamic effects of replacements of Pro residues in helix interiors of maltose-binding protein.

PubMed

Prajapati, R S; Lingaraju, G M; Bacchawat, Kiran; Surolia, Avadhesha; Varadarajan, Raghavan

2003-12-01

Introduction of Pro residues into helix interiors results in protein destabilization. It is currently unclear if the converse substitution (i.e., replacement of Pro residues that naturally occur in helix interiors would be stabilizing). Maltose-binding protein is a large 370-amino acid protein that contains 21 Pro residues. Of these, three nonconserved residues (P48, P133, and P159) occur at helix interiors. Each of the residues was replaced with Ala and Ser. Stabilities were characterized by differential scanning calorimetry (DSC) as a function of pH and by isothermal urea denaturation studies as a function of temperature. The P48S and P48A mutants were found to be marginally more stable than the wild-type protein. In the pH range of 5-9, there is an average increase in T(m) values of P48A and P48S of 0.4 degrees C and 0.2 degrees C, respectively, relative to the wild-type protein. The other mutants are less stable than the wild type. Analysis of the effects of such Pro substitutions in MBP and in three other proteins studied to date suggests that substitutions are more likely to be stabilizing if the carbonyl group i-3 or i-4 to the mutation site is not hydrogen bonded in the wild-type protein. Copyright 2003 Wiley-Liss, Inc.

Using Simple Quadratic Equations to Estimate Equilibrium Concentrations of an Acid

ERIC Educational Resources Information Center

Brilleslyper, Michael A.

2004-01-01

Application of quadratic equations to standard problem in chemistry like finding equilibrium concentrations of ions in an acid solution is explained. This clearly shows that pure mathematical analysis has meaningful applications in other areas as well.

Entanglement in a model for Hawking radiation: An application of quadratic algebras

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bambah, Bindu A., E-mail: bbsp@uohyd.ernet.in; Mukku, C., E-mail: mukku@iiit.ac.in; Shreecharan, T., E-mail: shreecharan@gmail.com

2013-03-15

Quadratic polynomially deformed su(1,1) and su(2) algebras are utilized in model Hamiltonians to show how the gravitational system consisting of a black hole, infalling radiation and outgoing (Hawking) radiation can be solved exactly. The models allow us to study the long-time behaviour of the black hole and its outgoing modes. In particular, we calculate the bipartite entanglement entropies of subsystems consisting of (a) infalling plus outgoing modes and (b) black hole modes plus the infalling modes, using the Janus-faced nature of the model. The long-time behaviour also gives us glimpses of modifications in the character of Hawking radiation. Finally, wemore » study the phenomenon of superradiance in our model in analogy with atomic Dicke superradiance. - Highlights: Black-Right-Pointing-Pointer We examine a toy model for Hawking radiation with quantized black hole modes. Black-Right-Pointing-Pointer We use quadratic polynomially deformed su(1,1) algebras to study its entanglement properties. Black-Right-Pointing-Pointer We study the 'Dicke Superradiance' in black hole radiation using quadratically deformed su(2) algebras. Black-Right-Pointing-Pointer We study the modification of the thermal character of Hawking radiation due to quantized black hole modes.« less

C-I···π Halogen Bonding Driven Supramolecular Helix of Bilateral N-Amidothioureas Bearing β-Turns.

PubMed

Cao, Jinlian; Yan, Xiaosheng; He, Wenbin; Li, Xiaorui; Li, Zhao; Mo, Yirong; Liu, Maili; Jiang, Yun-Bao

2017-05-17

We report the first example of C-I···π halogen bonding driven supramolecular helix in highly dilute solution of micromolar concentration, using alanine based bilateral I-substituted N-amidothioureas that contain helical fragments, the β-turn structures. The halogen bonding interactions afford head-to-tail linkages that help to propagate the helicity of the helical fragments. In support of this action of the halogen bonding, chiral amplification was observed in the supramolecular helix formed in acetonitrile solution. The present finding provides alternative tools in the design of self-assembling macromolecules.

Quadratic semiparametric Von Mises calculus

PubMed Central

Robins, James; Li, Lingling; Tchetgen, Eric

2009-01-01

We discuss a new method of estimation of parameters in semiparametric and nonparametric models. The method is based on U-statistics constructed from quadratic influence functions. The latter extend ordinary linear influence functions of the parameter of interest as defined in semiparametric theory, and represent second order derivatives of this parameter. For parameters for which the matching cannot be perfect the method leads to a bias-variance trade-off, and results in estimators that converge at a slower than n–1/2-rate. In a number of examples the resulting rate can be shown to be optimal. We are particularly interested in estimating parameters in models with a nuisance parameter of high dimension or low regularity, where the parameter of interest cannot be estimated at n–1/2-rate. PMID:23087487

A Conjugate Gradient Algorithm with Function Value Information and N-Step Quadratic Convergence for Unconstrained Optimization

PubMed Central

Li, Xiangrong; Zhao, Xupei; Duan, Xiabin; Wang, Xiaoliang

2015-01-01

It is generally acknowledged that the conjugate gradient (CG) method achieves global convergence—with at most a linear convergence rate—because CG formulas are generated by linear approximations of the objective functions. The quadratically convergent results are very limited. We introduce a new PRP method in which the restart strategy is also used. Moreover, the method we developed includes not only n-step quadratic convergence but also both the function value information and gradient value information. In this paper, we will show that the new PRP method (with either the Armijo line search or the Wolfe line search) is both linearly and quadratically convergent. The numerical experiments demonstrate that the new PRP algorithm is competitive with the normal CG method. PMID:26381742

A Conjugate Gradient Algorithm with Function Value Information and N-Step Quadratic Convergence for Unconstrained Optimization.

PubMed

Li, Xiangrong; Zhao, Xupei; Duan, Xiabin; Wang, Xiaoliang

2015-01-01

It is generally acknowledged that the conjugate gradient (CG) method achieves global convergence--with at most a linear convergence rate--because CG formulas are generated by linear approximations of the objective functions. The quadratically convergent results are very limited. We introduce a new PRP method in which the restart strategy is also used. Moreover, the method we developed includes not only n-step quadratic convergence but also both the function value information and gradient value information. In this paper, we will show that the new PRP method (with either the Armijo line search or the Wolfe line search) is both linearly and quadratically convergent. The numerical experiments demonstrate that the new PRP algorithm is competitive with the normal CG method.

QUADRATIC SERENDIPITY FINITE ELEMENTS ON POLYGONS USING GENERALIZED BARYCENTRIC COORDINATES.

PubMed

Rand, Alexander; Gillette, Andrew; Bajaj, Chandrajit

2014-01-01

We introduce a finite element construction for use on the class of convex, planar polygons and show it obtains a quadratic error convergence estimate. On a convex n -gon, our construction produces 2 n basis functions, associated in a Lagrange-like fashion to each vertex and each edge midpoint, by transforming and combining a set of n ( n + 1)/2 basis functions known to obtain quadratic convergence. The technique broadens the scope of the so-called 'serendipity' elements, previously studied only for quadrilateral and regular hexahedral meshes, by employing the theory of generalized barycentric coordinates. Uniform a priori error estimates are established over the class of convex quadrilaterals with bounded aspect ratio as well as over the class of convex planar polygons satisfying additional shape regularity conditions to exclude large interior angles and short edges. Numerical evidence is provided on a trapezoidal quadrilateral mesh, previously not amenable to serendipity constructions, and applications to adaptive meshing are discussed.

QUADRATIC SERENDIPITY FINITE ELEMENTS ON POLYGONS USING GENERALIZED BARYCENTRIC COORDINATES

PubMed Central

RAND, ALEXANDER; GILLETTE, ANDREW; BAJAJ, CHANDRAJIT

2013-01-01

We introduce a finite element construction for use on the class of convex, planar polygons and show it obtains a quadratic error convergence estimate. On a convex n-gon, our construction produces 2n basis functions, associated in a Lagrange-like fashion to each vertex and each edge midpoint, by transforming and combining a set of n(n + 1)/2 basis functions known to obtain quadratic convergence. The technique broadens the scope of the so-called ‘serendipity’ elements, previously studied only for quadrilateral and regular hexahedral meshes, by employing the theory of generalized barycentric coordinates. Uniform a priori error estimates are established over the class of convex quadrilaterals with bounded aspect ratio as well as over the class of convex planar polygons satisfying additional shape regularity conditions to exclude large interior angles and short edges. Numerical evidence is provided on a trapezoidal quadrilateral mesh, previously not amenable to serendipity constructions, and applications to adaptive meshing are discussed. PMID:25301974

The chromosomal mapping of four genes encoding winged helix proteins expressed early in mouse development

DOE Office of Scientific and Technical Information (OSTI.GOV)

Labosky, P.A.; Sakaki, Hiroshi; Hogan, B.L.M.

1996-06-01

Members of the winged helix family of transcription factors are required for the normal embryonic development of the mouse. Using the interspecific backcross panel from The Jackson Laboratory, we have determined the chromosomal locations of four genes that encode winged helix containing proteins. Mf1 was assigned to mouse Chromosome 8, Mf2 to Chromosome 4, Mf3 to Chromosome 9, and Mf4 to Chromosome 13. Since Mf3 is located in a region of Chromosome 9 containing many well-characterized mouse mutations such as short ear (se), ashen (ash), and dilute (d), we have analyzed deletion mutants to determine the location of Mf3 moremore » precisely. 14 refs., 3 figs.« less

Orientational preferences of neighboring helices can drive ER insertion of a marginally hydrophobic transmembrane helix

PubMed Central

Öjemalm, Karin; Halling, Katrin K.; Nilsson, IngMarie; von Heijne, Gunnar

2013-01-01

Summary α-helical integral membrane proteins critically depend on the correct insertion of their transmembrane α-helices into the lipid bilayer for proper folding, yet a surprisingly large fraction of the transmembrane α-helices in multispanning integral membrane proteins are not sufficiently hydrophobic to insert into the target membrane by themselves. How can such marginally hydrophobic segments nevertheless form transmembrane helices in the folded structure? Here, we show that a transmembrane helix with a strong orientational preference (Ncyt-Clum or Nlum-Ccyt) can both increase and decrease the hydrophobicity threshold for membrane insertion of a neighboring, marginally hydrophobic helix. This effect helps explain the ‘missing hydrophobicity’ in polytopic membrane proteins. PMID:22281052

The Use of GIS and Remotely Sensed Data in Environmental Public Health Tracking (EPHT): The HELIX-Atlanta Experience

NASA Technical Reports Server (NTRS)

Al-Hamdan, Mohammad Z.; Crosson, William L.; Limaye, Ashutosh S.; Estes, Maurice G., Jr.; Watts, Carol; Rickman, Douglas L.; Quattrochi, Dale A.; Qualters, Judith R.; Sinclair, Amber H.; Tolsma, Dennis D.;

Free Energy and Structure of Helix-forming Peptides: A Theoretical Investigation

NASA Astrophysics Data System (ADS)

Karpusenka, Vadzim

This thesis focuses on the structure and free energy of helical secondary structures of short peptides in a variety of experimental settings. Specifically, the formation of alpha-, pi- and 310-helices was investigated using large-scale classical molecular dynamics simulations with state-of-the-art force fields. In addition, the recently developed Adaptively Biased Molecular Dynamics (ABMD) and Steered Molecular Dynamics (SMD) methods were used to calculate the corresponding free energies. The most important results are as follows. For the examined peptide homopolymers, the observed minima on the free energy landscapes (based on suitable collective variables such as the radius of gyration, number of hydrogen bonds, and handedness) were associated with alpha-helices and "globular" or "knot-like" configurations only. No evidence was found to indicate that 310- or pi-helices represent equilibrium structures for these systems. In addition, the free energy landscape of short peptide chains formed by mixing two different amino acids were also examined. These results too indicate that the alpha-helix is only equilibrium helical secondary structure, and that the mixing of different amino acids does not result in the introduction of any significant new minima into the free energy landscapes. These results are in agreement with experimental observations insofar as these indicate that helical structural motifs are primary based on alpha-helices, with 310- and pi-helices being observed only rarely. Although pi- and 310-helices represent nonequilibrium structures, we were still able to estimate their free energies by means of SMD simulations. The helical secondary structure of the examined polypeptide chains is due to the formation of hydrogen bonds. However, there are other mechanisms that may allow for the additional stabilization of these structures. Specifically, in the so-called AK-(4,7) protein, the possible presence of disulfide bonds connecting cysteine residues may

Modelling Ocean Dissipation in Icy Satellites: A Comparison of Linear and Quadratic Friction

NASA Astrophysics Data System (ADS)

Hay, H.; Matsuyama, I.

2015-12-01

Although subsurface oceans are confirmed in Europa, Ganymede, Callisto, and strongly suspected in Enceladus and Titan, the exact mechanism required to heat and maintain these liquid reservoirs over Solar System history remains a mystery. Radiogenic heating can supply enough energy for large satellites whereas tidal dissipation provides the best explanation for the presence of oceans in small icy satellites. The amount of thermal energy actually contributed to the interiors of these icy satellites through oceanic tidal dissipation is largely unquantified. Presented here is a numerical model that builds upon previous work for quantifying tidally dissipated energy in the subsurface oceans of the icy satellites. Recent semi-analytical models (Tyler, 2008 and Matsuyama, 2014) have solved the Laplace Tidal Equations to estimate the time averaged energy flux over an orbital period in icy satellite oceans, neglecting the presence of a solid icy shell. These models are only able to consider linear Rayleigh friction. The numerical model presented here is compared to one of these semi-analytical models, finding excellent agreement between velocity and displacement solutions for all three terms to the tidal potential. Time averaged energy flux is within 2-6% of the analytical values. Quadratic (bottom) friction is then incorporated into the model, replacing linear friction. This approach is commonly applied to terrestrial ocean dissipation studies where dissipation scales nonlinearly with velocity. A suite of simulations are also run for the quadratic friction case which are then compared to and analysed against recent scaling laws developed by Chen and Nimmo (2013).

Applying the J-optimal channelized quadratic observer to SPECT myocardial perfusion defect detection

NASA Astrophysics Data System (ADS)

Kupinski, Meredith K.; Clarkson, Eric; Ghaly, Michael; Frey, Eric C.

2016-03-01

To evaluate performance on a perfusion defect detection task from 540 image pairs of myocardial perfusion SPECT image data we apply the J-optimal channelized quadratic observer (J-CQO). We compare AUC values of the linear Hotelling observer and J-CQO when the defect location is fixed and when it occurs in one of two locations. As expected, when the location is fixed a single channels maximizes AUC; location variability requires multiple channels to maximize the AUC. The AUC is estimated from both the projection data and reconstructed images. J-CQO is quadratic since it uses the first- and second- order statistics of the image data from both classes. The linear data reduction by the channels is described by an L x M channel matrix and in prior work we introduced an iterative gradient-based method for calculating the channel matrix. The dimensionality reduction from M measurements to L channels yields better estimates of these sample statistics from smaller sample sizes, and since the channelized covariance matrix is L x L instead of M x M, the matrix inverse is easier to compute. The novelty of our approach is the use of Jeffrey's divergence (J) as the figure of merit (FOM) for optimizing the channel matrix. We previously showed that the J-optimal channels are also the optimum channels for the AUC and the Bhattacharyya distance when the channel outputs are Gaussian distributed with equal means. This work evaluates the use of J as a surrogate FOM (SFOM) for AUC when these statistical conditions are not satisfied.

Three-dimensional simulation of helix traveling-wave tube cold-test characteristics using MAFIA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kory, C.L.

1996-12-31

A critically important step in the traveling-wave tube (TWT) design process is the cold-testing of the slow-wave circuit for dispersion, beam interaction impedance and RF losses. Experimental cold-tests can be very time-consuming and expensive, thus limiting the freedom to examine numerous variations to the test circuit. This makes the need for computational methods crucial as they can lower cost, reduce tube development time and allow the freedom to introduce novel and improved designs. The cold-test parameters have been calculated for a C-Band Northrop-Grumman helix TWT slow-wave circuit using MAFIA, the three-dimensional electromagnetic finite-integration computer code. Measured and simulated cold-test datamore » for the Northrop-Grumman helix TWT including dispersion, impedance and attenuation will be presented. Close agreement between simulated and measured values of the dispersion, impedance and attenuation has been obtained.« less

High-resolution orientation and depth of insertion of the voltage-sensing S4 helix of a potassium channel in lipid bilayers.

PubMed

Doherty, Tim; Su, Yongchao; Hong, Mei

2010-08-27

The opening and closing of voltage-gated potassium (Kv) channels are controlled by several conserved Arg residues in the S4 helix of the voltage-sensing domain. The interaction of these positively charged Arg residues with the lipid membrane has been of intense interest for understanding how membrane proteins fold to allow charged residues to insert into lipid bilayers against free-energy barriers. Using solid-state NMR, we have now determined the orientation and insertion depth of the S4 peptide of the KvAP channel in lipid bilayers. Two-dimensional (15)N correlation experiments of macroscopically oriented S4 peptide in phospholipid bilayers revealed a tilt angle of 40 degrees and two possible rotation angles differing by 180 degrees around the helix axis. Remarkably, the tilt angle and one of the two rotation angles are identical to those of the S4 helix in the intact voltage-sensing domain, suggesting that interactions between the S4 segment and other helices of the voltage-sensing domain are not essential for the membrane topology of the S4 helix. (13)C-(31)P distances between the S4 backbone and the lipid (31)P indicate a approximately 9 A local thinning and 2 A average thinning of the DMPC (1,2-dimyristoyl-sn-glycero-3-phosphochloline)/DMPG (1,2-dimyristoyl-sn-glycero-3-phosphatidylglycerol) bilayer, consistent with neutron diffraction data. Moreover, a short distance of 4.6 A from the guanidinium C(zeta) of the second Arg to (31)P indicates the existence of guanidinium phosphate hydrogen bonding and salt bridges. These data suggest that the structure of the Kv gating helix is mainly determined by protein-lipid interactions instead of interhelical protein-protein interactions, and the S4 amino acid sequence encodes sufficient information for the membrane topology of this crucial gating helix. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

SERS assay of telomerase activity at single-cell level and colon cancer tissues via quadratic signal amplification.

PubMed

Shi, Muling; Zheng, Jing; Liu, Changhui; Tan, Guixiang; Qing, Zhihe; Yang, Sheng; Yang, Jinfeng; Tan, Yongjun; Yang, Ronghua

2016-03-15

As an important biomarker and therapeutic target, telomerase has attracted extensive attention concerning its detection and monitoring. Recently, enzyme-assisted amplification approaches have provided useful platforms for the telomerase activity detection, however, further improvement in sensitivity is still hindered by the single-step signal amplification. Herein, we develop a quadratic signal amplification strategy for ultrasensitive surface-enhanced Raman scattering (SERS) detection of telomerase activity. The central idea of our design is using telomerase-induced silver nanoparticles (AgNPs) assembly and silver ions (Ag(+))-mediated cascade amplification. In our approach, each telomerase-aided DNA sequence extension could trigger the formation of a long double-stranded DNA (dsDNA), making numerous AgNPs assembling along with this long strand through specific Ag-S bond, to form a primary amplification element. For secondary amplification, each conjugated AgNP was dissolved into Ag(+), which can effectively induce the 4-aminobenzenethiol (4-ABT) modified gold nanoparticles (AuNPs@4-ABT) to undergo aggregation to form numerous "hot-spots". Through quadratic amplifications, a limit of detection down to single HeLa cell was achieved. More importantly, this method demonstrated good performance when applied to tissues from colon cancer patients, which exhibits great potential in the practical application of telomerase-based cancer diagnosis in early stages. To demonstrate the potential in screening the telomerase inhibitors and telomerase-targeted drugs, the proposed design is successfully employed to measure the inhibition of telomerase activity by 3'-azido-3'-deoxythymidine. Copyright © 2015 Elsevier B.V. All rights reserved.

Quadratic band touching points and flat bands in two-dimensional topological Floquet systems

NASA Astrophysics Data System (ADS)

Du, Liang; Zhou, Xiaoting; Fiete, Gregory A.

2017-01-01

In this paper we theoretically study, using Floquet-Bloch theory, the influence of circularly and linearly polarized light on two-dimensional band structures with Dirac and quadratic band touching points, and flat bands, taking the nearest neighbor hopping model on the kagome lattice as an example. We find circularly polarized light can invert the ordering of this three-band model, while leaving the flat band dispersionless. We find a small gap is also opened at the quadratic band touching point by two-photon and higher order processes. By contrast, linearly polarized light splits the quadratic band touching point (into two Dirac points) by an amount that depends only on the amplitude and polarization direction of the light, independent of the frequency, and generally renders dispersion to the flat band. The splitting is perpendicular to the direction of the polarization of the light. We derive an effective low-energy theory that captures these key results. Finally, we compute the frequency dependence of the optical conductivity for this three-band model and analyze the various interband contributions of the Floquet modes. Our results suggest strategies for optically controlling band structure and interaction strength in real systems.

Antimicrobial effects of helix D-derived peptides of human antithrombin III.

PubMed

Papareddy, Praveen; Kalle, Martina; Bhongir, Ravi K V; Mörgelin, Matthias; Malmsten, Martin; Schmidtchen, Artur

2014-10-24

Antithrombin III (ATIII) is a key antiproteinase involved in blood coagulation. Previous investigations have shown that ATIII is degraded by Staphylococcus aureus V8 protease, leading to release of heparin binding fragments derived from its D helix. As heparin binding and antimicrobial activity of peptides frequently overlap, we here set out to explore possible antibacterial effects of intact and degraded ATIII. In contrast to intact ATIII, the results showed that extensive degradation of the molecule yielded fragments with antimicrobial activity. Correspondingly, the heparin-binding, helix D-derived, peptide FFFAKLNCRLYRKANKSSKLV (FFF21) of human ATIII, was found to be antimicrobial against particularly the Gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa. Fluorescence microscopy and electron microscopy studies demonstrated that FFF21 binds to and permeabilizes bacterial membranes. Analogously, FFF21 was found to induce membrane leakage of model anionic liposomes. In vivo, FFF21 significantly reduced P. aeruginosa infection in mice. Additionally, FFF21 displayed anti-endotoxic effects in vitro. Taken together, our results suggest novel roles for ATIII-derived peptide fragments in host defense. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Linear-Quadratic Control of a MEMS Micromirror using Kalman Filtering

DTIC Science & Technology

2011-12-01

LINEAR-QUADRATIC CONTROL OF A MEMS MICROMIRROR USING KALMAN FILTERING THESIS Jamie P...A MEMS MICROMIRROR USING KALMAN FILTERING THESIS Presented to the Faculty Department of Electrical Engineering Graduate School of...actuated micromirrors fabricated by PolyMUMPs. Successful application of these techniques enables demonstration of smooth, stable deflections of 50% and

Estimation of positive semidefinite correlation matrices by using convex quadratic semidefinite programming.

PubMed

Fushiki, Tadayoshi

2009-07-01

The correlation matrix is a fundamental statistic that is used in many fields. For example, GroupLens, a collaborative filtering system, uses the correlation between users for predictive purposes. Since the correlation is a natural similarity measure between users, the correlation matrix may be used in the Gram matrix in kernel methods. However, the estimated correlation matrix sometimes has a serious defect: although the correlation matrix is originally positive semidefinite, the estimated one may not be positive semidefinite when not all ratings are observed. To obtain a positive semidefinite correlation matrix, the nearest correlation matrix problem has recently been studied in the fields of numerical analysis and optimization. However, statistical properties are not explicitly used in such studies. To obtain a positive semidefinite correlation matrix, we assume the approximate model. By using the model, an estimate is obtained as the optimal point of an optimization problem formulated with information on the variances of the estimated correlation coefficients. The problem is solved by a convex quadratic semidefinite program. A penalized likelihood approach is also examined. The MovieLens data set is used to test our approach.

Sequence and conformational preferences at termini of α-helices in membrane proteins: role of the helix environment.

PubMed

Shelar, Ashish; Bansal, Manju

2014-12-01

α-Helices are amongst the most common secondary structural elements seen in membrane proteins and are packed in the form of helix bundles. These α-helices encounter varying external environments (hydrophobic, hydrophilic) that may influence the sequence preferences at their N and C-termini. The role of the external environment in stabilization of the helix termini in membrane proteins is still unknown. Here we analyze α-helices in a high-resolution dataset of integral α-helical membrane proteins and establish that their sequence and conformational preferences differ from those in globular proteins. We specifically examine these preferences at the N and C-termini in helices initiating/terminating inside the membrane core as well as in linkers connecting these transmembrane helices. We find that the sequence preferences and structural motifs at capping (Ncap and Ccap) and near-helical (N' and C') positions are influenced by a combination of features including the membrane environment and the innate helix initiation and termination property of residues forming structural motifs. We also find that a large number of helix termini which do not form any particular capping motif are stabilized by formation of hydrogen bonds and hydrophobic interactions contributed from the neighboring helices in the membrane protein. We further validate the sequence preferences obtained from our analysis with data from an ultradeep sequencing study that identifies evolutionarily conserved amino acids in the rat neurotensin receptor. The results from our analysis provide insights for the secondary structure prediction, modeling and design of membrane proteins. © 2014 Wiley Periodicals, Inc.

Antagonistic Basic Helix-Loop-Helix/bZIP Transcription Factors Form Transcriptional Modules That Integrate Light and Reactive Oxygen Species Signaling in Arabidopsis[W

PubMed Central

Chen, Dongqin; Xu, Gang; Tang, Weijiang; Jing, Yanjun; Ji, Qiang; Fei, Zhangjun; Lin, Rongcheng

2013-01-01

The critical developmental switch from heterotrophic to autotrophic growth of plants involves light signaling transduction and the production of reactive oxygen species (ROS). ROS function as signaling molecules that regulate multiple developmental processes, including cell death. However, the relationship between light and ROS signaling remains unclear. Here, we identify transcriptional modules composed of the basic helix-loop-helix and bZIP transcription factors PHYTOCHROME-INTERACTING FACTOR1 (PIF1), PIF3, ELONGATED HYPOCOTYL5 (HY5), and HY5 HOMOLOGY (HYH) that bridge light and ROS signaling to regulate cell death and photooxidative response. We show that pif mutants release more singlet oxygen and exhibit more extensive cell death than the wild type during Arabidopsis thaliana deetiolation. Genome-wide expression profiling indicates that PIF1 represses numerous ROS and stress-related genes. Molecular and biochemical analyses reveal that PIF1/PIF3 and HY5/HYH physically interact and coordinately regulate the expression of five ROS-responsive genes by directly binding to their promoters. Furthermore, PIF1/PIF3 and HY5/HYH function antagonistically during the seedling greening process. In addition, phytochromes, cryptochromes, and CONSTITUTIVE PHOTOMORPHOGENIC1 act upstream to regulate ROS signaling. Together, this study reveals that the PIF1/PIF3-HY5/HYH transcriptional modules mediate crosstalk between light and ROS signaling and sheds light on a new mechanism by which plants adapt to the light environments. PMID:23645630

Disruption of alpha beta but not of gamma delta T cell development by overexpression of the helix-loop-helix protein Id3 in committed T cell progenitors.

PubMed Central

Blom, B; Heemskerk, M H; Verschuren, M C; van Dongen, J J; Stegmann, A P; Bakker, A Q; Couwenberg, F; Res, P C; Spits, H

1999-01-01

Enforced expression of Id3, which has the capacity to inhibit many basic helix-loop-helix (bHLH) transcription factors, in human CD34(+) hematopoietic progenitor cells that have not undergone T cell receptor (TCR) gene rearrangements inhibits development of the transduced cells into TCRalpha beta and gamma delta cells in a fetal thymic organ culture (FTOC). Here we document that overexpression of Id3, in progenitors that have initiated TCR gene rearrangements (pre-T cells), inhibits development into TCRalpha beta but not into TCRgamma delta T cells. Furthermore, Id3 impedes expression of recombination activating genes and downregulates pre-Talpha mRNA. These observations suggest possible mechanisms by which Id3 overexpression can differentially affect development of pre-T cells into TCRalpha beta and gamma delta cells. We also observed that cell surface CD4(-)CD8(-)CD3(-) cells with rearranged TCR genes developed from Id3-transduced but not from control-transduced pre-T cells in an FTOC. These cells had properties of both natural killer (NK) and pre-T cells. These findings suggest that bHLH factors are required to control T cell development after the T/NK developmental checkpoint. PMID:10329625

Basic helix-loop-helix transcription factor NEUROG1 and schizophrenia: effects on illness susceptibility, MRI brain morphometry and cognitive abilities.

PubMed

Ho, Beng-Choon; Epping, Eric; Wang, Kai; Andreasen, Nancy C; Librant, Amy; Wassink, Thomas H

2008-12-01

Transcription factors, including the basic helix-loop-helix (bHLH) family, regulate numerous genes and play vital roles in controlling gene expression. Consequently, transcription factor mutations can lead to phenotypic pleiotropy, and may be a candidate mechanism underlying the complex genetics and heterogeneous phenotype of schizophrenia. Neurogenin1 (NEUROG1; a.k.a. Ngn1 or Neurod3), a bHLH transcription factor encoded on a known schizophrenia linkage region in 5q31.1, induces glutamatergic and suppresses GABAergic neuronal differentiation during embryonic neurodevelopment. The goal of this study is to investigate NEUROG1 effects on schizophrenia risk and on phenotypic features of schizophrenia. We tested 392 patients with schizophrenia or schizoaffective disorder and 226 healthy normal volunteers for association with NEUROG1. Major alleles on two NEUROG1-associated SNPs (rs2344484-C-allele and rs8192558-G-allele) were significantly more prevalent among patients (p

Introduction of potential helix-capping residues into an engineered helical protein.

PubMed

Parker, M H; Hefford, M A

1998-08-01

MB-1 is an engineered protein that was designed to incorporate high percentages of four amino acid residues and to fold into a four-alpha-helix bundle motif. Mutations were made in the putative loop I and III regions of this protein with the aim of increasing the stability of the helix ends. Four variants, MB-3, MB-5, MB-11 and MB-13, have replacements intended to promote formation of an 'N-capping box'. The loop I and III sequences of MB-3 (both GDLST) and MB-11 (GGDST) were designed to cause alphaL C-terminal 'capping' motifs to form in helices I and III. MB-5 has a sequence, GPDST, that places proline in a favourable position for forming beta-turns, whereas MB-13 (GLDST) has the potential to form Schellman C-capping motifs. Size-exclusion chromatography suggested that MB-1, MB-3, MB-5, MB-11 and MB-13 all form dimers, or possibly trimers. Free energies for the unfolding of each of these variants were determined by urea denaturation, with the loss of secondary structure followed by CD spectroscopy. Assuming an equilibrium between folded dimer and unfolded monomer, MB-13 had the highest apparent stability (40.5 kJ/mol, with +/-2.5 kJ/mol 95% confidence limits), followed by MB-11 (39.3+/-5.9 kJ/mol), MB-3 (36.4+/-1.7 kJ/mol), MB-5 (34.7+/-2.1 kJ/mol) and MB-1 (29.3+/-1.3 kJ/mol); the same relative stabilities of the variants were found when a folded trimer to unfolded monomer model was used to calculate stabilities. All of the variants were relatively unstable for dimeric proteins, but were significantly more stable than MB-1. These findings suggest that it might be possible to increase the stability of a protein for which the three-dimensional structure is unknown by placing amino acid residues in positions that have the potential to form helix- and turn-stabilizing motifs.

The University in the Knowledge Economy: The Triple Helix Model and Its Implications

ERIC Educational Resources Information Center

Zheng, Peijun; Harris, Michael

2007-01-01

In the context of the global knowledge economy, the three major players--university, industry, and government--are becoming increasingly interdependent. As more intensified interactions and relationships of increasing complexity among the institutions evolve, the Triple Helix model attempts to describe not only interactions among university,…

Elegant Ince-Gaussian beams in a quadratic-index medium

NASA Astrophysics Data System (ADS)

Bai, Zhi-Yong; Deng, Dong-Mei; Guo, Qi

2011-09-01

Elegant Ince—Gaussian beams, which are the exact solutions of the paraxial wave equation in a quadratic-index medium, are derived in elliptical coordinates. These kinds of beams are the alternative form of standard Ince—Gaussian beams and they display better symmetry between the Ince-polynomials and the Gaussian function in mathematics. The transverse intensity distribution and the phase of the elegant Ince—Gaussian beams are discussed.

A quadratic regression modelling on paddy production in the area of Perlis

NASA Astrophysics Data System (ADS)

Goh, Aizat Hanis Annas; Ali, Zalila; Nor, Norlida Mohd; Baharum, Adam; Ahmad, Wan Muhamad Amir W.

2017-08-01

Polynomial regression models are useful in situations in which the relationship between a response variable and predictor variables is curvilinear. Polynomial regression fits the nonlinear relationship into a least squares linear regression model by decomposing the predictor variables into a kth order polynomial. The polynomial order determines the number of inflexions on the curvilinear fitted line. A second order polynomial forms a quadratic expression (parabolic curve) with either a single maximum or minimum, a third order polynomial forms a cubic expression with both a relative maximum and a minimum. This study used paddy data in the area of Perlis to model paddy production based on paddy cultivation characteristics and environmental characteristics. The results indicated that a quadratic regression model best fits the data and paddy production is affected by urea fertilizer application and the interaction between amount of average rainfall and percentage of area defected by pest and disease. Urea fertilizer application has a quadratic effect in the model which indicated that if the number of days of urea fertilizer application increased, paddy production is expected to decrease until it achieved a minimum value and paddy production is expected to increase at higher number of days of urea application. The decrease in paddy production with an increased in rainfall is greater, the higher the percentage of area defected by pest and disease.

Constraints on both the quadratic and quartic symmetry energy coefficients by 2β --decay energies

NASA Astrophysics Data System (ADS)

Wan, Niu; Xu, Chang; Ren, Zhongzhou; Liu, Jie

2018-05-01

In this Rapid Communication, the 2 β- -decay energies Q (2 β-) given in the atomic mass evaluation are used to extract not only the quadratic volume symmetry energy coefficient csymv, but also the quartic one csym,4 v. Based on the modified Bethe-Weizsäcker nuclear mass formula of the liquid-drop model, the decay energy Q (2 β-) is found to be closely related to both the quadratic and quartic symmetry energy coefficients csymv and csym,4 v. There are totally 449 data of decay energies Q (2 β-) used in the present analysis where the candidate nuclei are carefully chosen by fulfilling the following criteria: (1) large neutron-proton number difference N -Z , (2) large isospin asymmetry I , and (3) limited shell effect. The values of csymv and csym,4 v are extracted to be 29.345 and 3.634 MeV, respectively. Moreover, the quadratic surface-volume symmetry energy coefficient ratio is determined to be κ =csyms/csymv=1.356 .

QUADrATiC: scalable gene expression connectivity mapping for repurposing FDA-approved therapeutics.

PubMed

O'Reilly, Paul G; Wen, Qing; Bankhead, Peter; Dunne, Philip D; McArt, Darragh G; McPherson, Suzanne; Hamilton, Peter W; Mills, Ken I; Zhang, Shu-Dong

2016-05-04

Gene expression connectivity mapping has proven to be a powerful and flexible tool for research. Its application has been shown in a broad range of research topics, most commonly as a means of identifying potential small molecule compounds, which may be further investigated as candidates for repurposing to treat diseases. The public release of voluminous data from the Library of Integrated Cellular Signatures (LINCS) programme further enhanced the utilities and potentials of gene expression connectivity mapping in biomedicine. We describe QUADrATiC ( http://go.qub.ac.uk/QUADrATiC ), a user-friendly tool for the exploration of gene expression connectivity on the subset of the LINCS data set corresponding to FDA-approved small molecule compounds. It enables the identification of compounds for repurposing therapeutic potentials. The software is designed to cope with the increased volume of data over existing tools, by taking advantage of multicore computing architectures to provide a scalable solution, which may be installed and operated on a range of computers, from laptops to servers. This scalability is provided by the use of the modern concurrent programming paradigm provided by the Akka framework. The QUADrATiC Graphical User Interface (GUI) has been developed using advanced Javascript frameworks, providing novel visualization capabilities for further analysis of connections. There is also a web services interface, allowing integration with other programs or scripts. QUADrATiC has been shown to provide an improvement over existing connectivity map software, in terms of scope (based on the LINCS data set), applicability (using FDA-approved compounds), usability and speed. It offers potential to biological researchers to analyze transcriptional data and generate potential therapeutics for focussed study in the lab. QUADrATiC represents a step change in the process of investigating gene expression connectivity and provides more biologically-relevant results than

Design of Linear Quadratic Regulators and Kalman Filters

NASA Technical Reports Server (NTRS)

Lehtinen, B.; Geyser, L.

1986-01-01

AESOP solves problems associated with design of controls and state estimators for linear time-invariant systems. Systems considered are modeled in state-variable form by set of linear differential and algebraic equations with constant coefficients. Two key problems solved by AESOP are linear quadratic regulator (LQR) design problem and steady-state Kalman filter design problem. AESOP is interactive. User solves design problems and analyzes solutions in single interactive session. Both numerical and graphical information available to user during the session.

Field-antifield and BFV formalisms for quadratic systems with open gauge algebras

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nirov, K.S.; Razumov, A.V.

1992-09-20

In this paper the Lagrangian field-antifield (BV) and Hamiltonian (BFV) BRST formalisms for the general quadratic systems with open gauge algebra are considered. The equivalence between the Lagrangian and Hamiltonian formalisms is proven.

Numerical solution of quadratic matrix equations for free vibration analysis of structures

NASA Technical Reports Server (NTRS)

Gupta, K. K.

1975-01-01

This paper is concerned with the efficient and accurate solution of the eigenvalue problem represented by quadratic matrix equations. Such matrix forms are obtained in connection with the free vibration analysis of structures, discretized by finite 'dynamic' elements, resulting in frequency-dependent stiffness and inertia matrices. The paper presents a new numerical solution procedure of the quadratic matrix equations, based on a combined Sturm sequence and inverse iteration technique enabling economical and accurate determination of a few required eigenvalues and associated vectors. An alternative procedure based on a simultaneous iteration procedure is also described when only the first few modes are the usual requirement. The employment of finite dynamic elements in conjunction with the presently developed eigenvalue routines results in a most significant economy in the dynamic analysis of structures.

First report of soybean pest, Euschistus quadrator (Hempitera: pentatomidae) in Mississippi

USDA-ARS?s Scientific Manuscript database

Here we report on the first state and county record of Euschistus quadrator Ralston (Hemiptera: Pentatomidae) in Washington County, Mississippi. The species has been documented from Honduras to Virginia primarily on soybeans, cotton, various row crops, fruit, and non-crop hosts. The local impact...

Importance of the cutoff value in the quadratic adaptive integrate-and-fire model.

PubMed

Touboul, Jonathan

2009-08-01

The quadratic adaptive integrate-and-fire model (Izhikevich, 2003 , 2007 ) is able to reproduce various firing patterns of cortical neurons and is widely used in large-scale simulations of neural networks. This model describes the dynamics of the membrane potential by a differential equation that is quadratic in the voltage, coupled to a second equation for adaptation. Integration is stopped during the rise phase of a spike at a voltage cutoff value V(c) or when it blows up. Subsequently the membrane potential is reset, and the adaptation variable is increased by a fixed amount. We show in this note that in the absence of a cutoff value, not only the voltage but also the adaptation variable diverges in finite time during spike generation in the quadratic model. The divergence of the adaptation variable makes the system very sensitive to the cutoff: changing V(c) can dramatically alter the spike patterns. Furthermore, from a computational viewpoint, the divergence of the adaptation variable implies that the time steps for numerical simulation need to be small and adaptive. However, divergence of the adaptation variable does not occur for the quartic model (Touboul, 2008 ) and the adaptive exponential integrate-and-fire model (Brette & Gerstner, 2005 ). Hence, these models are robust to changes in the cutoff value.

Quadratic band touching points and flat bands in two-dimensional topological Floquet systems

NASA Astrophysics Data System (ADS)

Du, Liang; Zhou, Xiaoting; Fiete, Gregory; The CenterComplex Quantum Systems Team

In this work we theoretically study, using Floquet-Bloch theory, the influence of circularly and linearly polarized light on two-dimensional band structures with Dirac and quadratic band touching points, and flat bands, taking the nearest neighbor hopping model on the kagome lattice as an example. We find circularly polarized light can invert the ordering of this three band model, while leaving the flat-band dispersionless. We find a small gap is also opened at the quadratic band touching point by 2-photon and higher order processes. By contrast, linearly polarized light splits the quadratic band touching point (into two Dirac points) by an amount that depends only on the amplitude and polarization direction of the light, independent of the frequency, and generally renders dispersion to the flat band. The splitting is perpendicular to the direction of the polarization of the light. We derive an effective low-energy theory that captures these key results. Finally, we compute the frequency dependence of the optical conductivity for this 3-band model and analyze the various interband contributions of the Floquet modes. Our results suggest strategies for optically controlling band structure and interaction strength in real systems. We gratefully acknowledge funding from ARO Grant W911NF-14-1-0579 and NSF DMR-1507621.

Confidence set interference with a prior quadratic bound. [in geophysics

NASA Technical Reports Server (NTRS)

Backus, George E.

1989-01-01

Neyman's (1937) theory of confidence sets is developed as a replacement for Bayesian interference (BI) and stochastic inversion (SI) when the prior information is a hard quadratic bound. It is recommended that BI and SI be replaced by confidence set interference (CSI) only in certain circumstances. The geomagnetic problem is used to illustrate the general theory of CSI.

Basic Tilted Helix Bundle - a new protein fold in human FKBP25/FKBP3 and HectD1.

PubMed

Helander, Sara; Montecchio, Meri; Lemak, Alexander; Farès, Christophe; Almlöf, Jonas; Yi, Yanjun; Yee, Adelinda; Arrowsmith, Cheryl; DhePaganon, Sirano; Sunnerhagen, Maria

2014-04-25

In this paper, we describe the structure of a N-terminal domain motif in nuclear-localized FKBP251-73, a member of the FKBP family, together with the structure of a sequence-related subdomain of the E3 ubiquitin ligase HectD1 that we show belongs to the same fold. This motif adopts a compact 5-helix bundle which we name the Basic Tilted Helix Bundle (BTHB) domain. A positively charged surface patch, structurally centered around the tilted helix H4, is present in both FKBP25 and HectD1 and is conserved in both proteins, suggesting a conserved functional role. We provide detailed comparative analysis of the structures of the two proteins and their sequence similarities, and analysis of the interaction of the proposed FKBP25 binding protein YY1. We suggest that the basic motif in BTHB is involved in the observed DNA binding of FKBP25, and that the function of this domain can be affected by regulatory YY1 binding and/or interactions with adjacent domains. Copyright © 2014 Elsevier Inc. All rights reserved.

Chondrocutaneous helix rim advancement flap: two classical and two new modifications for very large defects of the ear.

PubMed

Valesky, E M; Kaufmann, R; Meissner, M

2015-11-01

The plastic reconstruction of the ear after microscopically controlled tumor surgery is a particular challenge. The chondrocutaneous helix rim advancement flap (CHRAF) is perfectly suited for the repair of different defects of the helix and even defects beyond. Here, we describe two known and two new modifications of the CHRAF that enlarge the scope of application in tumor surgery of the ear. We demonstrate the different techniques and practical application of the repair and evaluate the benefits and limitations. The CHRAF and its modifications is an excellent method for repair of various defects of the helical region of the ear. The CHRAF and its modifications proves to be an good alternative to other methods of closure by preserving the anatomical contour and mechanical and acoustic functions in a single-staged procedure with excellent aesthetic results. The two new modifications we introduced here, enlarge the known armentarium for very large defects of the upper pole and the mid-helix of the ear. © 2014 European Academy of Dermatology and Venereology.

Cooperative Solutions in Multi-Person Quadratic Decision Problems: Finite-Horizon and State-Feedback Cost-Cumulant Control Paradigm

DTIC Science & Technology

2007-01-01

CONTRACT NUMBER Problems: Finite -Horizon and State-Feedback Cost-Cumulant Control Paradigm (PREPRINT) 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER...cooperative cost-cumulant control regime for the class of multi-person single-objective decision problems characterized by quadratic random costs and... finite -horizon integral quadratic cost associated with a linear stochastic system . Since this problem formation is parameterized by the number of cost

Nonadiabatic rate constants for proton transfer and proton-coupled electron transfer reactions in solution: Effects of quadratic term in the vibronic coupling expansion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soudackov, Alexander; Hammes-Schiffer, Sharon

2015-11-17

Rate constant expressions for vibronically nonadiabatic proton transfer and proton-coupled electron transfer reactions are presented and analyzed. The regimes covered include electronically adiabatic and nonadiabatic reactions, as well as high-frequency and low-frequency regimes for the proton donor-acceptor vibrational mode. These rate constants differ from previous rate constants derived with the cumulant expansion approach in that the logarithmic expansion of the vibronic coupling in terms of the proton donor-acceptor distance includes a quadratic as well as a linear term. The analysis illustrates that inclusion of this quadratic term does not significantly impact the rate constants derived using the cumulant expansion approachmore » in any of the regimes studied. The effects of the quadratic term may become significant when using the vibronic coupling expansion in conjunction with a thermal averaging procedure for calculating the rate constant, however, particularly at high temperatures and for proton transfer interfaces with extremely soft proton donor-acceptor modes that are associated with extraordinarily weak hydrogen bonds. Even with the thermal averaging procedure, the effects of the quadratic term for weak hydrogen-bonding systems are less significant for more physically realistic models that prevent the sampling of unphysical short proton donor-acceptor distances, and the expansion of the coupling can be avoided entirely by calculating the couplings explicitly for the range of proton donor-acceptor distances. This analysis identifies the regimes in which each rate constant expression is valid and thus will be important for future applications to proton transfer and proton-coupled electron transfer in chemical and biological processes. We are grateful for support from National Institutes of Health Grant GM056207 (applications to enzymes) and the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of

Discrete-time Markovian-jump linear quadratic optimal control

NASA Technical Reports Server (NTRS)

Chizeck, H. J.; Willsky, A. S.; Castanon, D.

1986-01-01

This paper is concerned with the optimal control of discrete-time linear systems that possess randomly jumping parameters described by finite-state Markov processes. For problems having quadratic costs and perfect observations, the optimal control laws and expected costs-to-go can be precomputed from a set of coupled Riccati-like matrix difference equations. Necessary and sufficient conditions are derived for the existence of optimal constant control laws which stabilize the controlled system as the time horizon becomes infinite, with finite optimal expected cost.

Universality and diversity of folding mechanics for three-helix bundle proteins.

PubMed

Yang, Jae Shick; Wallin, Stefan; Shakhnovich, Eugene I

2008-01-22

In this study we evaluate, at full atomic detail, the folding processes of two small helical proteins, the B domain of protein A and the Villin headpiece. Folding kinetics are studied by performing a large number of ab initio Monte Carlo folding simulations using a single transferable all-atom potential. Using these trajectories, we examine the relaxation behavior, secondary structure formation, and transition-state ensembles (TSEs) of the two proteins and compare our results with experimental data and previous computational studies. To obtain a detailed structural information on the folding dynamics viewed as an ensemble process, we perform a clustering analysis procedure based on graph theory. Moreover, rigorous p(fold) analysis is used to obtain representative samples of the TSEs and a good quantitative agreement between experimental and simulated Phi values is obtained for protein A. Phi values for Villin also are obtained and left as predictions to be tested by future experiments. Our analysis shows that the two-helix hairpin is a common partially stable structural motif that gets formed before entering the TSE in the studied proteins. These results together with our earlier study of Engrailed Homeodomain and recent experimental studies provide a comprehensive, atomic-level picture of folding mechanics of three-helix bundle proteins.

A generalised optimal linear quadratic tracker with universal applications. Part 2: discrete-time systems

NASA Astrophysics Data System (ADS)

Ebrahimzadeh, Faezeh; Tsai, Jason Sheng-Hong; Chung, Min-Ching; Liao, Ying Ting; Guo, Shu-Mei; Shieh, Leang-San; Wang, Li

2017-01-01

Contrastive to Part 1, Part 2 presents a generalised optimal linear quadratic digital tracker (LQDT) with universal applications for the discrete-time (DT) systems. This includes (1) a generalised optimal LQDT design for the system with the pre-specified trajectories of the output and the control input and additionally with both the input-to-output direct-feedthrough term and known/estimated system disturbances or extra input/output signals; (2) a new optimal filter-shaped proportional plus integral state-feedback LQDT design for non-square non-minimum phase DT systems to achieve a minimum-phase-like tracking performance; (3) a new approach for computing the control zeros of the given non-square DT systems; and (4) a one-learning-epoch input-constrained iterative learning LQDT design for the repetitive DT systems.

The basic helix-loop-helix transcription factor Nex-1/Math-2 promotes neuronal survival of PC12 cells by modulating the dynamic expression of anti-apoptotic and cell cycle regulators

PubMed Central

Uittenbogaard, Martine; Chiaramello, Anne

2006-01-01

The basic helix-loop-helix transcription factor Nex1/Math-2 belongs to the NeuroD subfamily, which plays a critical role during neuronal differentiation and maintenance of the differentiated state. Previously, we demonstrated that Nex1 is a key regulatory component of the nerve growth factor (NGF) pathway. Further supporting this hypothesis, this study shows that Nex1 has survival-inducing properties similar to NGF, as Nex1-overexpressing PC12 cells survive in the absence of trophic factors. We dissected the molecular mechanism by which Nex1 confers neuroprotection upon serum removal and found that constitutive expression of Nex1 maintained the expression of specific G1 phase cyclin-dependent kinase inhibitors and concomitantly induced a dynamic expression profile of key anti-apoptotic regulators. This study provides the first evidence of the underlying mechanism by which a member of the NeuroD-subfamily promotes an active anti-apoptotic program essential to the survival of neurons. Our results suggest that the survival program may be viewed as an integral component of the intrinsic programming of the differ entiated state. PMID:15659228

The basic helix-loop-helix differentiation factor Nex1/MATH-2 functions as a key activator of the GAP-43 gene

PubMed Central

Uittenbogaard, Martine; Martinka, Debra L.; Chiaramello, Anne

2006-01-01

Nex1/MATH-2 is a neurogenic basic Helix-Loop-Helix (bHLH) transcription factor that belongs to the NeuroD subfamily. Its expression parallels that of the GAP-43 gene and peaks during brain development, when neurite outgrowth and synaptogenesis are highly active. We previously observed a direct correlation between the levels of expression of Nex1 and GAP-43 proteins, which resulted in extensive neurite outgrowth and neuronal differentiation of PC12 cells in the absence of nerve growth factor. Since the GAP-43 gene is a target for bHLH regulation, we investigated whether Nex1 could regulate the activity of the GAP-43 promoter. We found that among the members of the NeuroD subfamily, Nex1 promoted maximal activity of the GAP-43 promoter. The Nex1-mediated activity is restricted to the conserved E1–E2 cluster located near the major transcription start sites. By electrophoretic mobility shift assay and site-directed mutagenesis, we showed that Nex1 binds as homodimers and that the E1 E-box is a high affinity binding site. We further found that Nex1 released the ME1 E-protein-mediated repression in a concentration dependent manner. Thus, the E1–E2 cluster has a dual function: it can mediate activation or repression depending on the interacting bHLH proteins. Finally, a series of N-terminal and C-terminal deletions revealed that Nex1 transcriptional activity is linked to two distinct transactivation domains, TAD1 and TAD2, with TAD1 being unique to Nex1. Together, our results suggest that Nex1 may engage in selective interactions with components of the core transcriptional machinery whose assembly is dictated by the architecture of the GAP-43 promoter and cellular environment. PMID:12562512

The Basic Helix-Loop-Helix Transcription Factor MYC2 Directly Represses PLETHORA Expression during Jasmonate-Mediated Modulation of the Root Stem Cell Niche in Arabidopsis[W][OA

PubMed Central

Chen, Qian; Sun, Jiaqiang; Zhai, Qingzhe; Zhou, Wenkun; Qi, Linlin; Xu, Li; Wang, Bao; Chen, Rong; Jiang, Hongling; Qi, Jing; Li, Xugang; Palme, Klaus; Li, Chuanyou

2011-01-01

The root stem cell niche, which in the Arabidopsis thaliana root meristem is an area of four mitotically inactive quiescent cells (QCs) and the surrounding mitotically active stem cells, is critical for root development and growth. We report here that during jasmonate-induced inhibition of primary root growth, jasmonate reduces root meristem activity and leads to irregular QC division and columella stem cell differentiation. Consistently, jasmonate reduces the expression levels of the AP2-domain transcription factors PLETHORA1 (PLT1) and PLT2, which form a developmentally instructive protein gradient and mediate auxin-induced regulation of stem cell niche maintenance. Not surprisingly, the effects of jasmonate on root stem cell niche maintenance and PLT expression require the functioning of MYC2/JASMONATE INSENSITIVE1, a basic helix-loop-helix transcription factor that involves versatile aspects of jasmonate-regulated gene expression. Gel shift and chromatin immunoprecipitation experiments reveal that MYC2 directly binds the promoters of PLT1 and PLT2 and represses their expression. We propose that MYC2-mediated repression of PLT expression integrates jasmonate action into the auxin pathway in regulating root meristem activity and stem cell niche maintenance. This study illustrates a molecular framework for jasmonate-induced inhibition of root growth through interaction with the growth regulator auxin. PMID:21954460

Effects of hydrophobic helix length and side chain chemistry on biomimicry in peptoid analogues of SP-C.

PubMed

Brown, Nathan J; Wu, Cindy W; Seurynck-Servoss, Shannon L; Barron, Annelise E

2008-02-12

The hydrophobic proteins of lung surfactant (LS), SP-B and SP-C, are critical constituents of an effective surfactant replacement therapy for the treatment of respiratory distress syndrome. Because of concerns and difficulties associated with animal-derived surfactants, recent investigations have focused on the creation of synthetic analogues of the LS proteins. However, creating an accurate mimic of SP-C that retains its biophysical surface activity is extraordinarily challenging given the lipopeptide's extreme hydrophobicity and propensity to misfold and aggregate. One successful approach that overcomes these difficulties is the use of poly-N-substituted glycines, or peptoids, to mimic SP-C. To develop a non-natural, bioactive mimic of SP-C and to investigate the effects of side chain chemistry and length of the helical hydrophobic region, we synthesized, purified, and performed in vitro testing of two classes of peptoid SP-C mimics: those having a rigid alpha-chiral aromatic helix and those having a biomimetic alpha-chiral aliphatic helix. The length of the two classes of mimics was also systematically altered. Circular dichroism spectroscopy gave evidence that all of the peptoid-based mimics studied here emulated SP-C's secondary structure, forming stable helical structures in solution. Langmuir-Wilhelmy surface balance, fluorescence microscopy, and pulsating bubble surfactometry experiments provide evidence that the aromatic-based SP-C peptoid mimics, in conjunction with a synthetic lipid mixture, have superior surface activity and biomimetic film morphology in comparison to the aliphatic-based mimics and that there is an increase in surface activity corresponding to increasing helical length.