Fabrication and analysis of radiofrequency MEMS series capacitive single-pole double-throw switch

NASA Astrophysics Data System (ADS)

Bansal, Deepak; Bajpai, Anuroop; Kumar, Prem; Kaur, Maninder; Rangra, Kamaljit

2016-10-01

A compact radiofrequency (RF) MEMS single-pole double-throw (SPDT) switch based on series capacitive configuration is proposed. The critical process parameters are analyzed to improve the fabrication process. A technique of cold-hot thermal shock for lift-off method is explored. The residual stress in the structure is quantified by lancet test structures that come out to be 51 MPa. Effect of residual stress on actuation voltage is explored, which changes its value from 24 to 22 V. Resonance frequency and switching speed of the switch are 11 kHz and 44 μs, respectively, measured using laser Doppler vibrometer. Measured bandwidth of the SPDT switch is 20 GHz (5 to 25 GHz), which is verified with finite element method simulations in high frequency structure simulator©; and an equivalent LCR circuit in advanced design system©;. Insertion loss of the switch lies in -0.1 to -0.5 dB with isolation better than -20 dB for the above-mentioned bandwidth.

Theory of polymorphism in bacterial flagella

NASA Astrophysics Data System (ADS)

Powers, Thomas

2004-03-01

Escherichia coli and Salmonella swim using several flagella, each of which consists of a rotary motor, a universal joint known as the hook, and a helical filament which acts a propeller. The filament is normally left-handed in the absence of external stress, but undergoes mechanical phase transitions to other helical states ("polymorphs") in response to external torque. The filament is made of identical flagellin protein subunits which are organized into eleven protofilaments which wind around the filament. We develop an effective theory in which the flagellin subunits and their connections along the protofilaments are modelled with a double-well potential. A helical spring represents the other connections of the subunits, and introduces a twist-stretch coupling and an element of frustration in our model. We solve for the ground states and the phase diagram for filament shapes.

Controlled Photon Switch Assisted by Coupled Quantum Dots

PubMed Central

Luo, Ming-Xing; Ma, Song-Ya; Chen, Xiu-Bo; Wang, Xiaojun

2015-01-01

Quantum switch is a primitive element in quantum network communication. In contrast to previous switch schemes on one degree of freedom (DOF) of quantum systems, we consider controlled switches of photon system with two DOFs. These controlled photon switches are constructed by exploring the optical selection rules derived from the quantum-dot spins in one-sided optical microcavities. Several double controlled-NOT gate on different joint systems are greatly simplified with an auxiliary DOF of the controlling photon. The photon switches show that two DOFs of photons can be independently transmitted in quantum networks. This result reduces the quantum resources for quantum network communication. PMID:26095049

Controllable Magnetization Processes Induced by Nucleation Sites in Permalloy Rings

NASA Astrophysics Data System (ADS)

Chen, Ying-Jiun; Hsu, Chia-Jung; Liao, Chun-Neng; Huang, Hao-Ting; Lee, Chiun-Peng; Chiu, Yi-Hsun; Tung, Tzu-Yun; Lai, Mei-Feng

2010-02-01

Different arrangements of notches as nucleation sites are demonstrated experimentally and numerically to effectively control the magnetization processes of permalloy rings. In the ring with notches at the same side with respect to field direction, two same-helicity vortex domain walls in the onion state lead to two-step switching going through flux-closure state; in the ring with diagonal notches two opposite-helicity vortex domain walls lead to one-step switching skipping flux-closure state. The switching processes are repeatable in contrast to rings without notches where helicites of two vortex domain walls are random so the switching processes can not be controlled.

Valley-Selective Exciton Bistability in a Suspended Monolayer Semiconductor

NASA Astrophysics Data System (ADS)

Xie, Hongchao; Jiang, Shengwei; Shan, Jie; Mak, Kin Fai

2018-05-01

We demonstrate robust power- and wavelength-dependent optical bistability in fully suspended monolayers of WSe2 near the exciton resonance. Bistability has been achieved under continuous-wave optical excitation at an intensity level of 10^3 W/cm^2. The observed bistability is originated from a photo-thermal mechanism, which provides both optical nonlinearity and passive feedback, two essential elements for optical bistability. Under a finite magnetic field, the exciton bistability becomes helicity dependent, which enables repeatable switching of light purely by its polarization.

A remarkable solvent effect on the nuclearity of neutral titanium(IV)-based helicate assemblies.

PubMed

Weekes, David Michael; Diebold, Carine; Mobian, Pierre; Huguenard, Clarisse; Allouche, Lionel; Henry, Marc

2014-04-22

The spontaneous self-assembly of a neutral circular trinuclear Ti(IV) -based helicate is described through the reaction of titanium(IV) isopropoxide with a rationally designed tetraphenolic ligand. The trimeric ring helicate was obtained after diffusion of n-pentane into a solution with dichloromethane. The circular helicate has been characterized by using single-crystal X-ray diffraction study, (13) C CP-MAS NMR and (1) H NMR DOSY solution spectroscopic, and positive electrospray ionization mass-spectrometric analysis. These analytical data were compared with those obtained from a previously reported double-stranded helicate that crystallizes in toluene. The trimeric ring was unstable in a pure solution with dichloromethane and transformed into the double-stranded helicate. Thermodynamic analysis by means of the PACHA software revealed that formation of the double-stranded helicates was characterized by ΔH(toluene)=-30 kJ mol(-1) and ΔS(toluene)=+357 J K(-1)  mol(-1) , whereas these values were ΔH(CH2 Cl2 )=-75 kJ mol(-1) and ΔS(CH2 Cl2 )=-37 J K(-1)  mol(-1) for the ring helicate. The transformation of the ring helicate into the double-stranded helicate was a strongly endothermic process characterized by ΔH(CH2 Cl2 )=+127 kJ mol(-1) and ΔH(n-pentane)=+644 kJ mol(-1) associated with a large positive entropy change ΔS=+1115 J K(-1) ⋅mol(-1) . Consequently, the instability of the ring helicate in pure dichloromethane was attributed to the rather high dielectric constant and dipole moment of dichloromethane relative to n-pentane. Suggestions for increasing the stability of the ring helicate are given. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The HILDA Complex Coordinates a Conditional Switch in the 3′-Untranslated Region of the VEGFA mRNA

PubMed Central

Yao, Peng; Potdar, Alka A.; Ray, Partho Sarothi; Eswarappa, Sandeepa M.; Flagg, Andrew C.; Willard, Belinda; Fox, Paul L.

2013-01-01

Cell regulatory circuits integrate diverse, and sometimes conflicting, environmental cues to generate appropriate, condition-dependent responses. Here, we elucidate the components and mechanisms driving a protein-directed RNA switch in the 3′UTR of vascular endothelial growth factor (VEGF)-A. We describe a novel HILDA (hypoxia-inducible hnRNP L–DRBP76–hnRNP A2/B1) complex that coordinates a three-element RNA switch, enabling VEGFA mRNA translation during combined hypoxia and inflammation. In addition to binding the CA-rich element (CARE), heterogeneous nuclear ribonucleoprotein (hnRNP) L regulates switch assembly and function. hnRNP L undergoes two previously unrecognized, condition-dependent posttranslational modifications: IFN-γ induces prolyl hydroxylation and von Hippel-Lindau (VHL)-mediated proteasomal degradation, whereas hypoxia stimulates hnRNP L phosphorylation at Tyr359, inducing binding to hnRNP A2/B1, which stabilizes the protein. Also, phospho-hnRNP L recruits DRBP76 (double-stranded RNA binding protein 76) to the 3′UTR, where it binds an adjacent AU-rich stem-loop (AUSL) element, “flipping” the RNA switch by disrupting the GAIT (interferon-gamma-activated inhibitor of translation) element, preventing GAIT complex binding, and driving robust VEGFA mRNA translation. The signal-dependent, HILDA complex coordinates the function of a trio of neighboring RNA elements, thereby regulating translation of VEGFA and potentially other mRNA targets. The VEGFA RNA switch might function to ensure appropriate angiogenesis and tissue oxygenation during conflicting signals from combined inflammation and hypoxia. We propose the VEGFA RNA switch as an archetype for signal-activated, protein-directed, multi-element RNA switches that regulate posttranscriptional gene expression in complex environments. PMID:23976881

Passive micromixers with dual helical channels

NASA Astrophysics Data System (ADS)

Liu, Keyin; Yang, Qing; Chen, Feng; Zhao, Yulong; Meng, Xiangwei; Shan, Chao; Li, Yanyang

2015-02-01

In this study, a three-dimensional (3D) micromixer with cross-linked double helical microchannels is studied to achieve rapid mixing of fluids at low Reynolds numbers (Re). The 3D micromixer takes full advantages of the chaotic advection model with helical microchannels; meanwhile, the proposed crossing structure of double helical microchannels enables two flow patterns of repelling flow and straight flow in the fluids to promote the agitation effect. The complex 3D micromixer is realized by an improved femtosecond laser wet etching (FLWE) technology embedded in fused silica. The mixing results show that cross-linked double helical microchannels can achieve excellent mixing within 3 cycles (300 μm) over a wide range of low Re (1.5×10-3~600), which compare well with the conventional passive micromixers. This highly-effective micromixer is hoped to contribute to the integration of microfluidic systems.

Proof of principle in a de novo designed protein maquette: an allosterically regulated, charge-activated conformational switch in a tetra-alpha-helix bundle.

PubMed

Grosset, A M; Gibney, B R; Rabanal, F; Moser, C C; Dutton, P L

2001-05-08

New understanding of the engineering and allosteric regulation of natural protein conformational switches (such as those that couple chemical and ionic signals, mechanical force, and electro/chemical free energy for biochemical activation, catalysis, and motion) can be derived from simple de novo designed synthetic protein models (maquettes). We demonstrate proof of principle of both reversible switch action and allosteric regulation in a tetra-alpha-helical bundle protein composed of two identical di-helical subunits containing heme coordinated at a specific position close to the disulfide loop region. Individual bundles assume one of two switch states related by large-scale mechanical changes: a syn-topology (helices of the different subunits parallel) or anti-topology (helices antiparallel). Both the spectral properties of a coproporphyrin probe appended to the loop region and the distance-dependent redox interaction between the hemes identify the topologies. Beginning from a syn-topology, introduction of ferric heme in each subunit (either binding or redox change) shifts the topological balance by 25-50-fold (1.9-2.3 kcal/mol) to an anti-dominance. Charge repulsion between the two internal cationic ferric hemes drives the syn- to anti-switch, as demonstrated in two ways. When fixed in the syn-topology, the second ferric heme binding is 25-80-fold (1.9-2.6 kcal/mol) weaker than the first, and adjacent heme redox potentials are split by 80 mV (1.85 kcal/mol), values that energetically match the shift in topological balance. Allosteric and cooperative regulation of the switch by ionic strength exploits the shielded charge interactions between the two hemes and the exposed, cooperative interactions between the coproporphyrin carboxylates.

Magnetoresistance engineering and singlet/triplet switching in InAs nanowire quantum dots with ferromagnetic sidegates

NASA Astrophysics Data System (ADS)

Fábián, G.; Makk, P.; Madsen, M. H.; Nygârd, J.; Schönenberger, C.; Baumgartner, A.

2016-11-01

We present magnetoresistance (MR) experiments on an InAs nanowire quantum dot device with two ferromagnetic sidegates (FSGs) in a split-gate geometry. The wire segment can be electrically tuned to a single dot or to a double dot regime using the FSGs and a backgate. In both regimes we find a strong MR and a sharp MR switching of up to 25% at the field at which the magnetizations of the FSGs are inverted by the external field. The sign and amplitude of the MR and the MR switching can both be tuned electrically by the FSGs. In a double dot regime close to pinch-off we find two sharp transitions in the conductance, reminiscent of tunneling MR (TMR) between two ferromagnetic contacts, with one transition near zero and one at the FSG switching fields. These surprisingly rich characteristics we explain in several simple resonant tunneling models. For example, the TMR-like MR can be understood as a stray-field controlled transitions between singlet and triplet double dot states. Such local magnetic fields are the key elements in various proposals to engineer novel states of matter and may be used for testing electron spin based Bell inequalities.

Coulomb double helical structure

NASA Astrophysics Data System (ADS)

Kamimura, Tetsuo; Ishihara, Osamu

2012-01-01

Structures of Coulomb clusters formed by dust particles in a plasma are studied by numerical simulation. Our study reveals the presence of various types of self-organized structures of a cluster confined in a prolate spheroidal electrostatic potential. The stable configurations depend on a prolateness parameter for the confining potential as well as on the number of dust particles in a cluster. One-dimensional string, two-dimensional zigzag structure and three-dimensional double helical structure are found as a result of the transition controlled by the prolateness parameter. The formation of stable double helical structures resulted from the transition associated with the instability of angular perturbations on double strings. Analytical perturbation study supports the findings of numerical simulations.

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

Moroz, P.E.

A new stellarator configuration, the Double-Helix Stellarator (DHS), is introduced. This novel configuration features a double-helix center post as the only helical element of the stellarator coil system. The DHS configuration has many unique characteristics. One of them is the extreme low plasma aspect ratio, A {approx} 1--1.2. Other advantages include a high enclosed volume, appreciable rotational transform, and a possibility of extreme-high-{beta} MHD equilibria. Moreover, the DHS features improved transport characteristics caused by the absence of the magnetic field ripple on the outboard of the torus. Compactness, simplicity and modularity of the coil system add to the DHS advantagesmore » for fusion applications.« less

Double synchronized switch harvesting (DSSH): a new energy harvesting scheme for efficient energy extraction.

PubMed

Lallart, Mickaël; Garbuio, Lauric; Petit, Lionel; Richard, Claude; Guyomar, Daniel

2008-10-01

This paper presents a new technique for optimized energy harvesting using piezoelectric microgenerators called double synchronized switch harvesting (DSSH). This technique consists of a nonlinear treatment of the output voltage of the piezoelectric element. It also integrates an intermediate switching stage that ensures an optimal harvested power whatever the load connected to the microgenerator. Theoretical developments are presented considering either constant vibration magnitude, constant driving force, or independent extraction. Then experimental measurements are carried out to validate the theoretical predictions. This technique exhibits a constant output power for a wide range of load connected to the microgenerator. In addition, the extracted power obtained using such a technique allows a gain up to 500% in terms of maximal power output compared with the standard energy harvesting method. It is also shown that such a technique allows a fine-tuning of the trade-off between vibration damping and energy harvesting.

Novel polarization diversity without switch duplication of a Si-wire PILOSS optical switch.

PubMed

Tanizawa, Ken; Suzuki, Keijiro; Ikeda, Kazuhiro; Namiki, Shu; Kawashima, Hitoshi

2016-04-04

We demonstrate the compact polarization diversity based on the bidirectional full-port use of a path-independent-insertion-loss (PILOSS) optical switch. A polarization-diversity 4 × 4 strictly non-blocking optical switch is developed using a single thermooptic PILOSS Si-wire switch and fiber-based polarization beam splitters (PBSs) and combiners (PBCs). We measure characteristics of the switch and confirm that the proposed configuration demonstrates the performance in the insertion loss, polarization-dependent loss (PDL), and differential group delay (DGD) comparable with that of a conventional polarization-diversity 4 × 4 PILOSS switch using double switch elements. On the other hand, higher crosstalk is observed. The crosstalk increase is associated with the backward crosstalk at a waveguide intersection based on a directional coupler. The effect of the backward crosstalk on the total crosstalk is estimated, and future prospects are discussed.

Rearrangement of competing U2 RNA helices within the spliceosome promotes multiple steps in splicing

PubMed Central

Perriman, Rhonda J.; Ares, Manuel

2007-01-01

Nuclear pre-messenger RNA (pre-mRNA) splicing requires multiple spliceosomal small nuclear RNA (snRNA) and pre-mRNA rearrangements. Here we reveal a new snRNA conformational switch in which successive roles for two competing U2 helices, stem IIa and stem IIc, promote distinct splicing steps. When stem IIa is stabilized by loss of stem IIc, rapid ATP-independent and Cus2p-insensitive prespliceosome formation occurs. In contrast, hyperstabilized stem IIc improves the first splicing step on aberrant branchpoint pre-mRNAs and rescues temperature-sensitive U6–U57C, a U6 mutation that also suppresses first-step splicing defects of branchpoint mutations. A second, later role for stem IIa is revealed by its suppression of a cold-sensitive allele of the second-step splicing factor PRP16. Our data expose a spliceosomal progression cycle of U2 stem IIa formation, disruption by stem IIc, and then reformation of stem IIa before the second catalytic step. We propose that the competing stem IIa and stem IIc helices are key spliceosomal RNA elements that optimize juxtaposition of the proper reactive sites during splicing. PMID:17403781

Alpha3, a transposable element that promotes host sexual reproduction.

PubMed

Barsoum, Emad; Martinez, Paula; Aström, Stefan U

2010-01-01

Theoretical models predict that selfish DNA elements require host sex to persist in a population. Therefore, a transposon that induces sex would strongly favor its own spread. We demonstrate that a protein homologous to transposases, called alpha3, was essential for mating type switch in Kluyveromyces lactis. Mutational analysis showed that amino acids conserved among transposases were essential for its function. During switching, sequences in the 5' and 3' flanking regions of the alpha3 gene were joined, forming a DNA circle, showing that alpha3 mobilized from the genome. The sequences encompassing the alpha3 gene circle junctions in the mating type alpha (MATalpha) locus were essential for switching from MATalpha to MATa, suggesting that alpha3 mobilization was a coupled event. Switching also required a DNA-binding protein, Mating type switch 1 (Mts1), whose binding sites in MATalpha were important. Expression of Mts1 was repressed in MATa/MATalpha diploids and by nutrients, limiting switching to haploids in low-nutrient conditions. A hairpin-capped DNA double-strand break (DSB) was observed in the MATa locus in mre11 mutant strains, indicating that mating type switch was induced by MAT-specific DSBs. This study provides empirical evidence for selfish DNA promoting host sexual reproduction by mediating mating type switch.

Influence of ionic liquids on the syntheses and structures of Mn(II) coordination polymers based on multidentate N-heterocyclic aromatic ligands and bridging carboxylate ligands.

PubMed

Qin, Jian-Hua; Wang, Hua-Rui; Pan, Qi; Zang, Shuang-Quan; Hou, Hongwei; Fan, Yaoting

2015-10-28

Seven Mn(ii) coordination polymers, namely {[Mn2(ptptp)Cl2(H2O)3]·H2O}n (1), {[Mn(μ-ptptp)3]2[Mn3(μ3-Cl)]2}·2Cl·16H2O (2), {[Mn2(ptptp)(ip)2(H2O)3]·H2O}n (3), {[Mn2(ptptp)(5-CH3-ip)2(H2O)3]·H2O}n (4), {[Mn4(ptptp)(5-Br-ip)3(H2O)3]·4H2O}n (5), {[Mn2(ptptp)(Hbtc)(H2O)2]·2H2O}n (6) and {[Mn2(ptptp)(tdc)(H2O)2]·1.5H2O}n (7), have been prepared based on multidentate N-heterocyclic aromatic ligands and bridging carboxylate ligands (H2ptptp = 2-(5-{6-[5-(pyrazin-2-yl)-1H-1,2,4-triazol-3-yl]pyridin-2-yl}-1H-1,2,4-triazol-3-yl)pyrazine; R-isophthalic acids, H2ip-R: R = -H (3), -CH3 (4), -Br (5); H3btc = trimesic acid (6); H2tdc = thiophene-2,5-dicarboxylic acid (7)), in order to further probe the multiple roles of [RMI]Br ionic liquids in the hydro/solvothermal synthesis (RMI = 1-alkyl-3-methylimidazolium, R = ethyl, or propyl, or butyl). The successful syntheses of complexes 2-6 suggest that in hydro/solvothermal synthesis the addition of a small amount of [RMI]Br plays a crucial role. Complex 1 exhibits single right-handed helices constructed by ptptp ligands and Mn(ii) ions. Complex 2 possesses octanuclear helicate structures in which two propeller-shaped [Mn(μ-ptptp)3](4-) units embrace two [Mn3(μ3-Cl)](5+) cluster cores inside. Complexes 3 and 4 are isostructural and display a 1D double chain formed by two kinds of pseudo meso-helices: (Mn-ptptp)n and (Mn-5-R-ip)n. Complex 5 has a 2D structure containing 1D Mn(ii) ion chains formed through carboxylates and [ptptp](2-)-N,N bridges. Complex 6 shows a 2D structure formed by a meso-helix (Mn-ptptp)n and the partly deprotonated Hbtc ligands. Complex 7 features a heterochiral [2 + 2] coaxially nested double-helical column formed by using the outer double-helices (Mn-ptptp)n as a template to encapsulate the inner double-helices (Mn-tdc)n with opposite orientation. All complexes were characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis, single-crystal X-ray crystallography and powder X-ray diffraction. The magnetic properties of 1-7 were also investigated.

SiC MOSFET Switching Power Amplifier Project Summary

NASA Astrophysics Data System (ADS)

Miller, Kenneth E.; Ziemba, Timothy; Prager, James; Slobodov, Ilia; Henson, Alex

2017-10-01

Eagle Harbor Technologies has completed a Phase I/II program to develop SiC MOSFET based Switching Power Amplifiers (SPA) for precision magnet control in fusion science applications. During this program, EHT developed several units have been delivered to the Helicity Injected Torus (HIT) experiment at the University of Washington to drive both the voltage and flux circuits of the helicity injectors. These units are capable of switching 700 V at 100 kHz with an adjustable duty cycle from 10 - 90% and a combined total output current of 96 kA for 4 ms (at max current). The SPAs switching is controlled by the microcontroller at HIT, which adjusts the duty cycle to maintain a specific waveform in the injector. The SPAs include overcurrent and shoot-through protection circuity. EHT will present an overview of the program including final results for the SPA waveforms. With support of DOE SBIR.

Hydrodynamics of the double-wave structure of insect spermatozoa flagella

PubMed Central

Pak, On Shun; Spagnolie, Saverio E.; Lauga, Eric

2012-01-01

In addition to conventional planar and helical flagellar waves, insect sperm flagella have also been observed to display a double-wave structure characterized by the presence of two superimposed helical waves. In this paper, we present a hydrodynamic investigation of the locomotion of insect spermatozoa exhibiting the double-wave structure, idealized here as superhelical waves. Resolving the hydrodynamic interactions with a non-local slender body theory, we predict the swimming kinematics of these superhelical swimmers based on experimentally collected geometric and kinematic data. Our consideration provides insight into the relative contributions of the major and minor helical waves to swimming; namely, propulsion is owing primarily to the minor wave, with negligible contribution from the major wave. We also explore the dependence of the propulsion speed on geometric and kinematic parameters, revealing counterintuitive results, particularly for the case when the minor and major helical structures are of opposite chirality. PMID:22298815

The phosphorylation site in double helical amylopectin as investigated by a combined approach using chemical synthesis, crystallography and molecular modeling.

PubMed

Engelsen, Søren Balling; Madsen, Anders Østergaard; Blennow, Andreas; Motawia, Mohammed Saddik; Møller, Birger Lindberg; Larsen, Sine

2003-04-24

The only known in planta substitution of starch is phosphorylation. Whereas the function of starch phosphorylation is poorly understood, phosphorylated starch possesses improved functionality in vitro. Molecular models of native crystalline starch are currently being developed and the starch phosphorylating enzyme has recently been discovered. Accordingly, it is desirable to obtain a more exact description of the molecular structures of phosphorylated starch. We have determined the crystal structure of methyl alpha-D-glucopyranoside 6-O-phosphate as its potassium salt which is thought to be the starch phosphate counterion in vivo. From this structure and previously known glucophosphate structures we describe the possible 6-O-phosphate geometries and through modeling extrapolate the results to the double helical structure of the crystalline part of amylopectin. The geometries of the existing crystal structures of 6-O-phosphate groups were found to belong to two main adiabatic valleys. One of these conformations could be fitted into the double helical amylopectin part without perturbing the double helical amylopectin structure and without creating steric problems for the hexagonal chain-chain packing.

Reduction of Helicity-Dependent Instrumental Laser Intensity Asymmetries

NASA Astrophysics Data System (ADS)

Burtwistle, Samantha; Dreiling, Joan; Gay, Timothy

2014-05-01

We present a new optical system that greatly reduces helicity-dependent instrumental intensity asymmetries. The optical setup is similar to that described in Fabrikant et al., where two beams with orthogonal linear polarizations are sent through a chopper, allowing only one beam to pass through the optical system at a time. The two temporally-separated beams are then spatially recombined. We now use a system, with a second active polarization changing element, that is analogous to that described in Gay and Dunning, which compensates for false asymmetries in Mott polarimetry. In our setup, the orthogonal linear polarizations are now circularly polarized by a Pockels cell switching between a retardance of + λ /4 and - λ/4 at the same frequency as the chopper, but with a 90-degree phase shift. Using this method, we have been able to control the standard deviation of the mean of our asymmetries, as measured by a photodiode with lock-in signal processing, to 3*10-8.

Unfolding of a branched double-helical DNA three-way junction with triple-helical ends.

PubMed

Hüsler, P L; Klump, H H

1994-08-15

We have designed three oligonucleotides (33 mers) which when mixed in a 1:1:1 ratio form double-helical DNA three-way junctions with triple helical ends in the pH interval pH 4 to 5.5. The triplex to coil transition is initiated by raising the temperature and was recorded by temperature gradient gel electrophoresis, uv melting, and differential scanning calorimetry. The transitions can be deconvoluted into three subtransitions representing the independent thermal denaturation of each of the arms. We have proposed a model for the unfolding pathway and give the thermodynamic parameters for each step as calculated using the formalism outlined in the appendix.

Modified Involute Helical Gears: Computerized Design, Simulation of Meshing, and Stress Analysis

NASA Technical Reports Server (NTRS)

Handschuh, Robert (Technical Monitor); Litvin, Faydor L.; Gonzalez-Perez, Ignacio; Carnevali, Luca; Kawasaki, Kazumasa; Fuentes-Aznar, Alfonso

2003-01-01

The computerized design, methods for generation, simulation of meshing, and enhanced stress analysis of modified involute helical gears is presented. The approaches proposed for modification of conventional involute helical gears are based on conjugation of double-crowned pinion with a conventional helical involute gear. Double-crowning of the pinion means deviation of cross-profile from an involute one and deviation in longitudinal direction from a helicoid surface. Using the method developed, the pinion-gear tooth surfaces are in point-contact, the bearing contact is localized and oriented longitudinally, and edge contact is avoided. Also, the influence of errors of aligment on the shift of bearing contact, vibration, and noise are reduced substantially. The theory developed is illustrated with numerical examples that confirm the advantages of the gear drives of the modified geometry in comparison with conventional helical involute gears.

Modified Involute Helical Gears: Computerized Design, Simulation of Meshing and Stress Analysis

NASA Technical Reports Server (NTRS)

2003-01-01

The computerized design, methods for generation, simulation of meshing, and enhanced stress analysis of modified involute helical gears is presented. The approaches proposed for modification of conventional involute helical gears are based on conjugation of double-crowned pinion with a conventional helical involute gear. Double-crowning of the pinion means deviation of cross-profile from an involute one and deviation in longitudinal direction from a helicoid surface. Using the method developed, the pinion-gear tooth surfaces are in point-contact, the bearing contact is localized and oriented longitudinally, and edge contact is avoided. Also, the influence of errors of alignment on the shift of bearing contact, vibration, and noise are reduced substantially. The theory developed is illustrated with numerical examples that confirm the advantages of the gear drives of the modified geometry in comparison with conventional helical involute gears.

Compensatory Evolution of Intrinsic Transcription Terminators in Bacillus Cereus

PubMed Central

Safina, Ksenia R.; Mironov, Andrey A.

2017-01-01

Many RNA molecules possess complicated secondary structure critical to their function. Mutations in double-helical regions of RNA may disrupt Watson–Crick (WC) interactions causing structure destabilization or even complete loss of function. Such disruption can be compensated by another mutation restoring base pairing, as has been shown for mRNA, rRNA and tRNA. Here, we investigate the evolution of intrinsic transcription terminators between closely related strains of Bacillus cereus. While the terminator structure is maintained by strong natural selection, as evidenced by the low frequency of disrupting mutations, we observe multiple instances of pairs of disrupting-compensating mutations in RNA structure stems. Such two-step switches between different WC pairs occur very fast, consistent with the low fitness conferred by the intermediate non-WC variant. Still, they are not instantaneous, and probably involve transient fixation of the intermediate variant. The GU wobble pair is the most frequent intermediate, and remains fixed longer than other intermediates, consistent with its less disruptive effect on the RNA structure. Double switches involving non-GU intermediates are more frequent at the ends of RNA stems, probably because they are associated with smaller fitness loss. Together, these results show that the fitness landscape of bacterial transcription terminators is rather rugged, but that the fitness valleys associated with unpaired stem nucleotides are rather shallow, facilitating evolution. PMID:28201729

Self-assembly of 3,5-bis(ethoxycarbonyl)pyrazolate anions and ammonium cations of beta-phenylethylamine or homoveratrylamine into hetero-double-stranded helical structures.

PubMed

Reviriego, Felipe; Sanz, Ana; Navarro, Pilar; Latorre, Julio; García-España, Enrique; Liu-Gonzalez, Malva

2009-08-21

Hydrogen-bonded double-stranded hetero-helices are formed when reacting sodium 3,5-bis(ethoxycarbonyl)pyrazolate with beta-phenethylammonium or homoveratrylammonium chloride, in which one of the strands is defined by the ammonium cations and the other one by the pyrazolate anions.

Triplex-forming oligonucleotides: a third strand for DNA nanotechnology

PubMed Central

2018-01-01

Abstract DNA self-assembly has proved to be a useful bottom-up strategy for the construction of user-defined nanoscale objects, lattices and devices. The design of these structures has largely relied on exploiting simple base pairing rules and the formation of double-helical domains as secondary structural elements. However, other helical forms involving specific non-canonical base-base interactions have introduced a novel paradigm into the process of engineering with DNA. The most notable of these is a three-stranded complex generated by the binding of a third strand within the duplex major groove, generating a triple-helical (‘triplex’) structure. The sequence, structural and assembly requirements that differentiate triplexes from their duplex counterparts has allowed the design of nanostructures for both dynamic and/or structural purposes, as well as a means to target non-nucleic acid components to precise locations within a nanostructure scaffold. Here, we review the properties of triplexes that have proved useful in the engineering of DNA nanostructures, with an emphasis on applications that hitherto have not been possible by duplex formation alone. PMID:29228337

Molecular Structure of a Helical ribbon in a Peptide Self-Assembly

NASA Astrophysics Data System (ADS)

Hwang, Wonmuk; Marini, Davide; Kamm, Roger D.; Zhang, Shuguang

2002-03-01

We have studied the molecular structure of nanometer scale helical ribbons observed during self-assembly of the peptide KFE8 (amino acid sequence: FKFEFKFE) (NanoLetters (2002, in press)). By analyzing the hydrogen bonding patterns between neighboring peptide backbones, we constructed a number of possible β-sheets. Using all possible combinations of these, we built helical ribbons with dimensions close to those found experimentally and performed molecular dynamics simulations to identify the most stable structure. Solvation effects were implemented by the analytic continuum electrostatics (ACE) model developed by Schaefer and Karplus (J. Phys. Chem. 100, 1578 (1996)). By applying electrostatic double layer theory, we incorporated the effect of pH by scaling the amount of charge on the sidechains. Our results suggest that the helical ribbon is comprised of a double β-sheet where the inner and the outer helices have distinct hydrogen bonding patterns. Our approach has general applicability to the study of helices formed by the self-assembly of β-sheet forming peptides with various amino acid sequences.

Double Helical Gear Performance Results in High Speed Gear Trains

NASA Technical Reports Server (NTRS)

Handschuh, Robert F.; Ehinger, Ryan; Sinusas, Eric; Kilmain, Charles

2009-01-01

The operation of high speed gearing systems in the transmissions of tiltrotor aircraft has an effect on overall propulsion system efficiency. Recent work has focused on many aspects of high-speed helical gear trains as would be used in tiltrotor aircraft such as operational characteristics, comparison of analytical predictions to experimental data and the affect of superfinishing on transmission performance. Baseline tests of an aerospace quality system have been conducted in the NASA Glenn High-Speed Helical Gear Train Test Facility and have been described in earlier studies. These earlier tests had utilized single helical gears. The results that will be described in this study are those attained using double helical gears. This type of gear mesh can be configured in this facility to either pump the air-oil environment from the center gap between the meshing gears to the outside of tooth ends or in the reverse direction. Tests were conducted with both inward and outward air-oil pumping directions. Results are compared to the earlier baseline results of single helical gears.

Double Helical Gear Performance Results in High Speed Gear Trains

NASA Technical Reports Server (NTRS)

Handschuh, Robert F.; Ehinger, Ryan; Sinusas, Eric; Kilmain, Charles

2010-01-01

The operation of high speed gearing systems in the transmissions of tiltrotor aircraft has an effect on overall propulsion system efficiency. Recent work has focused on many aspects of high-speed helical gear trains as would be used in tiltrotor aircraft such as operational characteristics, comparison of analytical predictions to experimental data and the affect of superfinishing on transmission performance. Baseline tests of an aerospace quality system have been conducted in the NASA Glenn High-Speed Helical Gear Train Test Facility and have been described in earlier studies. These earlier tests had utilized single helical gears. The results that will be described in this study are those attained using double helical gears. This type of gear mesh can be configured in this facility to either pump the air-oil environment from the center gap between the meshing gears to the outside of tooth ends or in the reverse direction. Tests were conducted with both inward and outward air-oil pumping directions. Results are compared to the earlier baseline results of single helical gears.

Triple helical DNA in a duplex context and base pair opening

PubMed Central

Esguerra, Mauricio; Nilsson, Lennart; Villa, Alessandra

2014-01-01

It is fundamental to explore in atomic detail the behavior of DNA triple helices as a means to understand the role they might play in vivo and to better engineer their use in genetic technologies, such as antigene therapy. To this aim we have performed atomistic simulations of a purine-rich antiparallel triple helix stretch of 10 base triplets flanked by canonical Watson–Crick double helices. At the same time we have explored the thermodynamic behavior of a flipping Watson–Crick base pair in the context of the triple and double helix. The third strand can be accommodated in a B-like duplex conformation. Upon binding, the double helix changes shape, and becomes more rigid. The triple-helical region increases its major groove width mainly by oversliding in the negative direction. The resulting conformations are somewhere between the A and B conformations with base pairs remaining almost perpendicular to the helical axis. The neighboring duplex regions maintain a B DNA conformation. Base pair opening in the duplex regions is more probable than in the triplex and binding of the Hoogsteen strand does not influence base pair breathing in the neighboring duplex region. PMID:25228466

Noncovalent Interactions in the Asymmetric Synthesis of Rigid, Conjugated Helical Structures

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

Miyasaka, Makoto; Pink, Maren; Rajca, Suchada

Tetrakis({beta}-trithiophene) 1 folds into a helical conformation (RRR) that facilitates double ring annelation, with high diastereoselectivity and modest enantioselectivity, to provide bis[7]helicene 2 (MRM). This rigid, helically locked structure has enhanced chiroptical properties similar to the corresponding [15]helicene.

A 3D Model of Double-Helical DNA Showing Variable Chemical Details

ERIC Educational Resources Information Center

Cady, Susan G.

2005-01-01

Since the first DNA model was created approximately 50 years ago using molecular models, students and teachers have been building simplified DNA models from various practical materials. A 3D double-helical DNA model, made by placing beads on a wire and stringing beads through holes in plastic canvas, is described. Suggestions are given to enhance…

A widespread family of serine/threonine protein phosphatases shares a common regulatory switch with proteasomal proteases

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

Bradshaw, Niels; Levdikov, Vladimir M.; Zimanyi, Christina M.

PP2C phosphatases control biological processes including stress responses, development, and cell division in all kingdoms of life. Diverse regulatory domains adapt PP2C phosphatases to specific functions, but how these domains control phosphatase activity was unknown. We present structures representing active and inactive states of the PP2C phosphatase SpoIIE from Bacillus subtilis. Based on structural analyses and genetic and biochemical experiments, we identify an α-helical switch that shifts a carbonyl oxygen into the active site to coordinate a metal cofactor. Our analysis indicates that this switch is widely conserved among PP2C family members, serving as a platform to control phosphatase activitymore » in response to diverse inputs. Remarkably, the switch is shared with proteasomal proteases, which we identify as evolutionary and structural relatives of PP2C phosphatases. Although these proteases use an unrelated catalytic mechanism, rotation of equivalent helices controls protease activity by movement of the equivalent carbonyl oxygen into the active site.« less

RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs.

PubMed

Bhattacharyya, Dhananjay; Halder, Sukanya; Basu, Sankar; Mukherjee, Debasish; Kumar, Prasun; Bansal, Manju

2017-02-01

Comprehensive analyses of structural features of non-canonical base pairs within a nucleic acid double helix are limited by the availability of a small number of three dimensional structures. Therefore, a procedure for model building of double helices containing any given nucleotide sequence and base pairing information, either canonical or non-canonical, is seriously needed. Here we describe a program RNAHelix, which is an updated version of our widely used software, NUCGEN. The program can regenerate duplexes using the dinucleotide step and base pair orientation parameters for a given double helical DNA or RNA sequence with defined Watson-Crick or non-Watson-Crick base pairs. The original structure and the corresponding regenerated structure of double helices were found to be very close, as indicated by the small RMSD values between positions of the corresponding atoms. Structures of several usual and unusual double helices have been regenerated and compared with their original structures in terms of base pair RMSD, torsion angles and electrostatic potentials and very high agreements have been noted. RNAHelix can also be used to generate a structure with a sequence completely different from an experimentally determined one or to introduce single to multiple mutation, but with the same set of parameters and hence can also be an important tool in homology modeling and study of mutation induced structural changes.

Magnetics and Power System Upgrades for the Pegasus-U Experiment

NASA Astrophysics Data System (ADS)

Preston, R. C.; Bongard, M. W.; Fonck, R. J.; Lewicki, B. T.

2014-10-01

To support the missions of developing local helicity injection startup and exploiting advanced tokamak physics studies at near unity aspect ratio, the proposed Pegasus-U will include expanded magnetic systems and associated power supplies. A new centerstack increases the toroidal field seven times to 1 T and the volt-seconds by a factor of six while maintaining operation at an aspect ratio of 1.2. The poloidal field magnet system is expanded to support improved shape control and robust double or single null divertor operation at the full plasma current of 0.3 MA. An integrated digital control system based on Field Programmable Gate Arrays (FPGAs) provides active feedback control of all magnet currents. Implementation of the FPGAs is achieved with modular noise reducing electronics. The digital feedback controllers replace the existing analog systems and switch multiplexing technology. This will reduce noise sensitivity and allow the operational Ohmic power supply voltage to increase from 2100 V to its maximum capacity of 2400 V. The feedback controller replacement also allows frequency control for ``freewheeling''--stopping the switching for a short interval and allowing the current to coast. The FPGAs assist in optimizing pulse length by having programmable switching events to minimize energy losses. They also allow for more efficient switching topologies that provide improved stored energy utilization, and support increasing the pulse length from 25 ms to 50-100 ms. Work supported by US DOE Grant DE-FG02-96ER54375.

High-Power Actuation from Molecular Photoswitches in Enantiomerically Paired Soft Springs.

PubMed

Aßhoff, Sarah J; Lancia, Federico; Iamsaard, Supitchaya; Matt, Benjamin; Kudernac, Tibor; Fletcher, Stephen P; Katsonis, Nathalie

2017-03-13

Motion in plants often relies on dynamic helical systems as seen in coiling tendrils, spasmoneme springs, and the opening of chiral seedpods. Developing nanotechnology that would allow molecular-level phenomena to drive such movements in artificial systems remains a scientific challenge. Herein, we describe a soft device that uses nanoscale information to mimic seedpod opening. The system exploits a fundamental mechanism of stimuli-responsive deformation in plants, namely that inflexible elements with specific orientations are integrated into a stimuli-responsive matrix. The device is operated by isomerization of a light-responsive molecular switch that drives the twisting of strips of liquid-crystal elastomers. The strips twist in opposite directions and work against each other until the pod pops open from stress. This mechanism allows the photoisomerization of molecular switches to stimulate rapid shape changes at the macroscale and thus to maximize actuation power. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Left Ventricular Retraining and Double Switch in Patients With Congenitally Corrected Transposition of the Great Arteries.

PubMed

Ibrahimiye, Ali N; Mainwaring, Richard D; Patrick, William L; Downey, Laura; Yarlagadda, Vamsi; Hanley, Frank L

2017-03-01

Congenitally corrected transposition of the great arteries (CC-TGA) is a complex form of congenital heart defect with numerous anatomic subgroups. The majority of patients with CC-TGA are excellent candidates for a double-switch procedure. However, in the absence of an unrestrictive ventricular septal defect or subpulmonary stenosis, the left ventricle (LV) may undergo involution and require retraining prior to double switch. The purpose of this study was to review our experience with patients having CC-TGA who required LV retraining prior to a double-switch procedure. This was a retrospective review of 24 patients with CC-TGA who were enrolled in an LV retraining program in preparation for a double-switch procedure. The median age at the time of enrollment for retraining was 11 months (range 1 month-24 years). The average left ventricle to right ventricle pressure ratio was 0.39 ± 0.07 prior to intervention. All 24 patients underwent placement of an initial pulmonary artery band (PAB) for LV retraining. Eighteen (75%) of the 24 patients underwent a double-switch procedure with no operative mortality. Of these 18 patients, 9 had a single PAB and 9 required a second band for retraining. Six patients have not undergone a double-switch procedure to date. Five patients are good candidates for a double switch and are 2 weeks, 3 weeks, 4 weeks, 8 months, and 35 months since their last PAB. One patient died from a noncardiac cause 26 months after PAB retightening. The 18 patients who underwent a double switch were followed for an average of 5 ± 1 years (range 0.1-10.3 years). There has been no late mortality, and only 2 patients required further reinterventions. The data demonstrate that LV retraining has been highly effective in this select group of patients with CC-TGA. The data also demonstrate that the results of the double-switch procedure have been excellent at midterm follow-up. These results suggest that LV retraining and double switch offer a reliable strategy option for patients with CC-TGA.

Interplay between negative and positive design elements in Gα helical domains of G proteins determines interaction specificity towards RGS2.

PubMed

Kasom, Mohammad; Gharra, Samia; Sadiya, Isra; Avital-Shacham, Meirav; Kosloff, Mickey

2018-06-20

Regulators of G protein Signaling (RGS) proteins inactivate Gα subunits, thereby controling G protein-coupled signaling networks. Among all RGS proteins, RGS2 is unique in interacting only with the Gα q and not with the Gα i sub-family. Previous studies suggested that this specificity is determined by the RGS domain, and in particular by three RGS2-specific residues that lead to a unique mode of interaction with Gα q This interaction was further proposed to act through contacts with the Gα GTPase domain. Here, we combined energy calculations and GTPase activity measurements to determine which Gα residues dictate specificity toward RGS2. We identified putative specificity-determining residues in the Gα helical domain, which among G proteins is found only in Gα subunits. Replacing these helical domain residues in Gα i with their Gα q counterparts resulted in a dramatic specificity-switch towards RGS2. We further show that Gα-RGS2 specificity is set by Gα i residues that perturb interactions with RGS2, and by Gα q residues that enhance these interactions. These results show, for the first time, that the Gα helical domain is central to dictating specificity towards RGS2, suggesting this domain plays a general role in governing Gα-RGS specificity. Our insights provide new options for manipulating RGS-G protein interactions in vivo , for better understanding of their "wiring" into signaling networks, and for devising novel drugs targeting such interactions. ©2018 The Author(s).

A widespread family of serine/threonine protein phosphatases shares a common regulatory switch with proteasomal proteases

PubMed Central

Bradshaw, Niels; Levdikov, Vladimir M; Zimanyi, Christina M; Gaudet, Rachelle; Wilkinson, Anthony J; Losick, Richard

2017-01-01

PP2C phosphatases control biological processes including stress responses, development, and cell division in all kingdoms of life. Diverse regulatory domains adapt PP2C phosphatases to specific functions, but how these domains control phosphatase activity was unknown. We present structures representing active and inactive states of the PP2C phosphatase SpoIIE from Bacillus subtilis. Based on structural analyses and genetic and biochemical experiments, we identify an α-helical switch that shifts a carbonyl oxygen into the active site to coordinate a metal cofactor. Our analysis indicates that this switch is widely conserved among PP2C family members, serving as a platform to control phosphatase activity in response to diverse inputs. Remarkably, the switch is shared with proteasomal proteases, which we identify as evolutionary and structural relatives of PP2C phosphatases. Although these proteases use an unrelated catalytic mechanism, rotation of equivalent helices controls protease activity by movement of the equivalent carbonyl oxygen into the active site. DOI: http://dx.doi.org/10.7554/eLife.26111.001 PMID:28527238

Single helically folded aromatic oligoamides that mimic the charge surface of double-stranded B-DNA

NASA Astrophysics Data System (ADS)

Ziach, Krzysztof; Chollet, Céline; Parissi, Vincent; Prabhakaran, Panchami; Marchivie, Mathieu; Corvaglia, Valentina; Bose, Partha Pratim; Laxmi-Reddy, Katta; Godde, Frédéric; Schmitter, Jean-Marie; Chaignepain, Stéphane; Pourquier, Philippe; Huc, Ivan

2018-05-01

Numerous essential biomolecular processes require the recognition of DNA surface features by proteins. Molecules mimicking these features could potentially act as decoys and interfere with pharmacologically or therapeutically relevant protein-DNA interactions. Although naturally occurring DNA-mimicking proteins have been described, synthetic tunable molecules that mimic the charge surface of double-stranded DNA are not known. Here, we report the design, synthesis and structural characterization of aromatic oligoamides that fold into single helical conformations and display a double helical array of negatively charged residues in positions that match the phosphate moieties in B-DNA. These molecules were able to inhibit several enzymes possessing non-sequence-selective DNA-binding properties, including topoisomerase 1 and HIV-1 integrase, presumably through specific foldamer-protein interactions, whereas sequence-selective enzymes were not inhibited. Such modular and synthetically accessible DNA mimics provide a versatile platform to design novel inhibitors of protein-DNA interactions.

Solid-state switch increases switching speed

NASA Technical Reports Server (NTRS)

Mcgowan, G. F.

1966-01-01

Solid state switch for commutating capacitors in an RC commutated network increases switching speed and extends the filtering or commutating frequency spectrum well into the kilocycle region. The switch is equivalent to the standard double- pole double-throw /DPDT/ relay and is driven from digital micrologic circuits.

Foldback intercoil DNA and the mechanism of DNA transposition.

PubMed

Kim, Byung-Dong

2014-09-01

Foldback intercoil (FBI) DNA is formed by the folding back at one point of a non-helical parallel track of double-stranded DNA at as sharp as 180° and the intertwining of two double helixes within each other's major groove to form an intercoil with a diameter of 2.2 nm. FBI DNA has been suggested to mediate intra-molecular homologous recombination of a deletion and inversion. Inter-molecular homologous recombination, known as site-specific insertion, on the other hand, is mediated by the direct perpendicular approach of the FBI DNA tip, as the attP site, onto the target DNA, as the attB site. Transposition of DNA transposons involves the pairing of terminal inverted repeats and 5-7-bp tandem target duplication. FBI DNA configuration effectively explains simple as well as replicative transposition, along with the involvement of an enhancer element. The majority of diverse retrotransposable elements that employ a target site duplication mechanism is also suggested to follow the FBI DNA-mediated perpendicular insertion of the paired intercoil ends by non-homologous end-joining, together with gap filling. A genome-wide perspective of transposable elements in light of FBI DNA is discussed.

Period doubling induced by thermal noise amplification in genetic circuits.

PubMed

Ruocco, G; Fratalocchi, A

2014-11-18

Rhythms of life are dictated by oscillations, which take place in a wide rage of biological scales. In bacteria, for example, oscillations have been proven to control many fundamental processes, ranging from gene expression to cell divisions. In genetic circuits, oscillations originate from elemental block such as autorepressors and toggle switches, which produce robust and noise-free cycles with well defined frequency. In some circumstances, the oscillation period of biological functions may double, thus generating bistable behaviors whose ultimate origin is at the basis of intense investigations. Motivated by brain studies, we here study an "elemental" genetic circuit, where a simple nonlinear process interacts with a noisy environment. In the proposed system, nonlinearity naturally arises from the mechanism of cooperative stability, which regulates the concentration of a protein produced during a transcription process. In this elemental model, bistability results from the coherent amplification of environmental fluctuations due to a stochastic resonance of nonlinear origin. This suggests that the period doubling observed in many biological functions might result from the intrinsic interplay between nonlinearity and thermal noise.

Stimuli-Driven Control of the Helical Axis of Self-Organized Soft Helical Superstructures.

PubMed

Bisoyi, Hari Krishna; Bunning, Timothy J; Li, Quan

2018-06-01

Supramolecular and macromolecular functional helical superstructures are ubiquitous in nature and display an impressive catalog of intriguing and elegant properties and performances. In materials science, self-organized soft helical superstructures, i.e., cholesteric liquid crystals (CLCs), serve as model systems toward the understanding of morphology- and orientation-dependent properties of supramolecular dynamic helical architectures and their potential for technological applications. Moreover, most of the fascinating device applications of CLCs are primarily determined by different orientations of the helical axis. Here, the control of the helical axis orientation of CLCs and its dynamic switching in two and three dimensions using different external stimuli are summarized. Electric-field-, magnetic-field-, and light-irradiation-driven orientation control and reorientation of the helical axis of CLCs are described and highlighted. Different techniques and strategies developed to achieve a uniform lying helix structure are explored. Helical axis control in recently developed heliconical cholesteric systems is examined. The control of the helical axis orientation in spherical geometries such as microdroplets and microshells fabricated from these enticing photonic fluids is also explored. Future challenges and opportunities in this exciting area involving anisotropic chiral liquids are then discussed. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electro-optic control of a PPLN-unpoled LiNbO3 boundary for low-voltage Q switching of an intracavity frequency-doubled Nd3+:YVO4 laser.

PubMed

Torregrosa, A J; Maestre, H; Fernández-Pousa, C R; Pereda, J A; Capmany, J

2009-08-01

We present a simple technique to integrate an electro-optic Q switch in a periodically poled bulk lithium niobate crystal bounded by two unpoled (monodomain) regions. The technique exploits the high sensitivity to low applied electric fields of the total internal reflection condition in the periodic poled-unpoled boundary for the small grazing incidence angles associated with the diffraction of a focused Gaussian beam that propagates in the periodically poled region with its axis parallel to the boundary. When the arrangement is placed intracavity to a 1064 nm diode-pumped Nd(3+):YVO(4) laser, it performs simultaneously as a Q switch and as a second-harmonic generator, with Q switching starting at applied voltages as low as 1 V over a 500 microm thickness and with no additional optical elements.

[DNA structure from A to Z--biological implications of structural diversity of DNA].

PubMed

Bukowiecka-Matusiak, Małgorzata; Woźniak, Lucyna A

2006-01-01

Deoxyribonucleic acid (DNA) is a biopolymer of nucleotides, usually adopting a double-stranded helical form in cells, with complementary base pairing holding the two strands together. The most stable is B-DNA conformation, although numerous other double helical structures can occur under specific conditions (A-DNA, Z-DNA, P-DNA). The existence of multiple-stranded (triplex, tetraplex) forms in vivo and their biological function in cells are subject of intensive studies.

The dominant role of side chains in supramolecular double helical organisation in synthetic tripeptides

NASA Astrophysics Data System (ADS)

Sharma, Ankita; Tiwari, Priyanka; Dutt Konar, Anita

2018-06-01

Peptide self-assembled nanostructures have attracted attention recently owing to their promising applications in diversified avenues. To validate the importance of sidechains in supramolecular architectural stabilization, herein this report describes the self-assembly propensities involving weak interactions in a series of model tripeptides Boc-Xaa-Aib-Yaa-OMe I-IV, (where Xaa = 4-F-Phe/NMeSer/Ile & Yaa = Tyr in peptide I-III respectively and Xaa = 4-F-Phe & Yaa = Ile in peptide IV) differing in terminal side chains. The solid state structural analysis reveals that tripeptide (I) displays supramolecular preference for double helical architecture. However, when slight modification has been introduced in the N-terminal side chains disfavour the double helical organisation (Peptide II and III). Indeed the peptides display sheet like ensemble within the framework. Besides replacement of C-terminal Tyr by Ile in peptide I even do not promote the architecture, emphasizing the dominant role of balance of side chains in stabilizing double helical organisation. The CD measurements, concentration dependant studies, NMR titrations and ROESY spectra are well in agreement with the solid state conformational investigation. Moreover the morphological experiments utilizing FE-SEM, support the heterogeneity present in the peptides. Thus this work may not only hold future promise in understanding the structure and function of neurodegenerative diseases but also assist in rational design of protein modification in biologically active peptides.

Microsecond kinetics in model single- and double-stranded amylose polymers.

PubMed

Sattelle, Benedict M; Almond, Andrew

2014-05-07

Amylose, a component of starch with increasing biotechnological significance, is a linear glucose polysaccharide that self-organizes into single- and double-helical assemblies. Starch granule packing, gelation and inclusion-complex formation result from finely balanced macromolecular kinetics that have eluded precise experimental quantification. Here, graphics processing unit (GPU) accelerated multi-microsecond aqueous simulations are employed to explore conformational kinetics in model single- and double-stranded amylose. The all-atom dynamics concur with prior X-ray and NMR data while surprising and previously overlooked microsecond helix-coil, glycosidic linkage and pyranose ring exchange are hypothesized. In a dodecasaccharide, single-helical collapse was correlated with linkages and rings transitioning from their expected syn and (4)C1 chair conformers. The associated microsecond exchange rates were dependent on proximity to the termini and chain length (comparing hexa- and trisaccharides), while kinetic features of dodecasaccharide linkage and ring flexing are proposed to be a good model for polymers. Similar length double-helices were stable on microsecond timescales but the parallel configuration was sturdier than the antiparallel equivalent. In both, tertiary organization restricted local chain dynamics, implying that simulations of single amylose strands cannot be extrapolated to dimers. Unbiased multi-microsecond simulations of amylose are proposed as a valuable route to probing macromolecular kinetics in water, assessing the impact of chemical modifications on helical stability and accelerating the development of new biotechnologies.

Finite element analysis of helical flows in human aortic arch: A novel index

PubMed Central

Lee, Cheng-Hung; Liu, Kuo-Sheng; Jhong, Guan-Heng; Liu, Shih-Jung; Hsu, Ming-Yi; Wang, Chao-Jan; Hung, Kuo-Chun

2014-01-01

This study investigates the helical secondary flows in the aortic arch using finite element analysis. The relationship between helical flow and the configuration of the aorta in patients of whose three-dimensional images constructed from computed tomography scans was examined. A finite element model of the pressurized root, arch, and supra-aortic vessels was developed to simulate the pattern of helical secondary flows. Calculations indicate that most of the helical secondary flow was formed in the ascending aorta. Angle α between the zero reference point and the aortic ostium (correlation coefficient (r) = −0.851, P = 0.001), the dispersion index of the cross section of the ascending (r = 0.683, P = 0.021) and descending aorta (r = 0.732, P = 0.010), all correlated closely with the presence of helical flow (P < 0.05). Stepwise multiple linear regression analysis confirmed angel α to be independently associated with the helical flow pattern in therein (standardized coefficients = −0.721, P = 0.023). The presence of helical fluid motion based on the atherosclerotic risks of patients, including those associated with diabetes, hypertension, hyperlipidemia, or renal insufficiency, was also evaluated. Numerical simulation of the flow patterns in aortas incorporating the atherosclerotic risks may better explain the mechanism of formation of helical flows and provide insight into causative factors that underlie them. PMID:24803960

Molecular structure of r/GCG/d/TATACGC/ - A DNA-RNA hybrid helix joined to double helical DNA

NASA Technical Reports Server (NTRS)

Wang, A. H.-J.; Fujii, S.; Rich, A.; Van Boom, J. H.; Van Der Marel, G. A.; Van Boeckel, S. A. A.

1982-01-01

The molecule r(GCG)d(TATACGC) is self-complementary and forms two DNA-RNA hybrid segments surrounding a central region of double helical DNA; its molecular structure has been solved by X-ray analysis. All three parts of the molecule adopt a conformation which is close to that seen in the 11-fold RNA double helix. The conformation of the ribonucleotides is partly determined by water molecules bridging between the ribose O2' hydroxyl group and cytosine O2. The hybrid-DNA duplex junction contains no structural discontinuities. However, the central DNA TATA sequence has some structural irregularities.

Ultrastructural organization of connective tissue microfibrils in the posterior chamber of the eye in vivo and in vitro.

PubMed

Inoue, S

1995-02-01

The ultrastructural organization of connective tissue microfibrils was studied in the mouse eye and also by means of in vitro experiments for reconstituting microfibrils. In the posterior chamber of the eye of the C57BL/6J mouse, 3 nm-wide ribbon-like double-tracked structures were present and were periodically associated on either side with 3.5 nm-wide particulate structures identified as pentosomes, the subunits of amyloid P component (AP). At certain sites, such composite structures were observed in various stages of helical winding, and in these helices, pentosomes were preferentially localized internally. In helices in the final stages of winding, the resulting rods appeared increasingly similar to those of microfibrils. In experiments in vitro, incubation of chondroitin sulfate proteoglycan (CSPG) in TRIS buffer, pH 7.4, at 35 degrees C for 1 h produced random aggregates of 3 nm-wide double-tracked structures similar to those observed in the eye. Co-incubation of CSPG and AP resulted in the formation of rod-like structures arranged parallel to one another in approximately 50 nm-thick sheet-like layers. These rods were ultrastructurally similar to microfibrils and were made up of helically wound, 3 nm-wide double-tracked structures containing pentosomes within their core. The results of in vivo as well as in vitro experiments suggest the possibility that the connective tissue microfibril is composed of helically wound, CSPG-containing, 3 nm-wide double-tracked structures periodically associated with pentosomes which, as the helix becomes progressively tighter, fit with one another at the core of the helix to form successive 8.5 nm-wide disks of AP segments.

Increasing the magnetic helicity content of a plasma by pulsing a magnetized source.

PubMed

Woodruff, S; Stallard, B W; McLean, H S; Hooper, E B; Bulmer, R; Cohen, B I; Hill, D N; Holcomb, C T; Moller, J; Wood, R D

2004-11-12

By operating a magnetized coaxial gun in a pulsed mode it is possible to produce large voltage pulses of duration approximately 500 mus while reaching a few kV, giving a discrete input of helicity into a spheromak. In the sustained spheromak physics experiment (SSPX), it is observed that pulsing serves to nearly double the stored magnetic energy and double the temperature. We discuss these results by comparison with 3D MHD simulations of the same phenomenon.

New Methods for Improved Double Circular-Arc Helical Gears

NASA Technical Reports Server (NTRS)

Litvin, Faydor L.; Lu, Jian

1997-01-01

The authors have extended the application of double circular-arc helical gears for internal gear drives. The geometry of the pinion and gear tooth surfaces has been determined. The influence of errors of alignment on the transmission errors and the shift of the bearing contact have been investigated. Application of a predesigned parabolic function for the reduction of transmission errors was proposed. Methods of grinding of the pinion-gear tooth surfaces by a disk-shaped tool and a grinding worm were proposed.

Visualization of vortex structures and analysis of frequency of PVC

NASA Astrophysics Data System (ADS)

Gesheva, E. S.; Shtork, S. I.; Alekseenko, S. V.

2018-03-01

The paper presents the results of the study of large-scale vortex structures in a model chamber. Methods of forming quasi-stationary vortices of various shapes by changing the geometric parameters of the chamber have been proposed. In the model chamber with a tangential swirl of the flow, a rectilinear vortex, single helical and double helical vortices were obtained. The double helical structure of the vortex is unique due to its immovability around the axis of the chamber. The resulting structures slowly oscillate around their own axes, which is called the vortex core precession; while the oscillation frequency depends linearly on the liquid flow rate. The use of stationary vortex structures in power plants will increase the efficiency of combustion chambers and reduce slagging.

Transposable genetic elements in Spirulina and potential applications for genetic engineering

NASA Astrophysics Data System (ADS)

Hiroyuki, Kojima; Qin, Song; Thankappan, Ajith Kumar; Yoshikazu, Kawata; Shin-Ichi, Yano

1998-03-01

Transposable elements in cyanobacteria are briefly reviewed. Evidence is presented to show that transposable elements in Spirulina platensis is actually reflected on the phenotype change, i e., helical to straight filaments. Transposition intermediates of DNA were isolated from the extrachromosome and the transposition was related to helical variations in Spirulina. Uses of transposable elements for microalgal recombination are discussed based on the transposition mechanism.

Insights into the Photoprotective Switch of the Major Light-harvesting Complex II (LHCII)

PubMed Central

Sunku, Kiran; de Groot, Huub. J. M.; Pandit, Anjali

2013-01-01

Light-harvesting antennae of the LHC family form transmembrane three-helix bundles of which two helices are interlocked by conserved arginine-glutamate (Arg-Glu) ion pairs that form ligation sites for chlorophylls. The antenna proteins of photosystem II have an intriguing dual function. In excess light, they can switch their conformation from a light-harvesting into a photoprotective state, in which the excess and harmful excitation energies are safely dissipated as heat. Here we applied magic angle spinning NMR and selective Arg isotope enrichment as a noninvasive method to analyze the Arg structures of the major light-harvesting complex II (LHCII). The conformations of the Arg residues that interlock helix A and B appear to be preserved in the light-harvesting and photoprotective state. Several Arg residues have very downfield-shifted proton NMR responses, indicating that they stabilize the complex by strong hydrogen bonds. For the Arg Cα chemical shifts, differences are observed between LHCII in the active, light-harvesting and in the photoprotective, quenched state. These differences are attributed to a conformational change of the Arg residue in the stromal loop region. We conclude that the interlocked helices of LHCII form a rigid core. Consequently, the LHCII conformational switch does not involve changes in A/B helix tilting but likely involves rearrangements of the loops and helical segments close to the stromal and lumenal ends. PMID:23629658

Helicity multiplexed broadband metasurface holograms.

PubMed

Wen, Dandan; Yue, Fuyong; Li, Guixin; Zheng, Guoxing; Chan, Kinlong; Chen, Shumei; Chen, Ming; Li, King Fai; Wong, Polis Wing Han; Cheah, Kok Wai; Pun, Edwin Yue Bun; Zhang, Shuang; Chen, Xianzhong

2015-09-10

Metasurfaces are engineered interfaces that contain a thin layer of plasmonic or dielectric nanostructures capable of manipulating light in a desirable manner. Advances in metasurfaces have led to various practical applications ranging from lensing to holography. Metasurface holograms that can be switched by the polarization state of incident light have been demonstrated for achieving polarization multiplexed functionalities. However, practical application of these devices has been limited by their capability for achieving high efficiency and high image quality. Here we experimentally demonstrate a helicity multiplexed metasurface hologram with high efficiency and good image fidelity over a broad range of frequencies. The metasurface hologram features the combination of two sets of hologram patterns operating with opposite incident helicities. Two symmetrically distributed off-axis images are interchangeable by controlling the helicity of the input light. The demonstrated helicity multiplexed metasurface hologram with its high performance opens avenues for future applications with functionality switchable optical devices.

Helicity multiplexed broadband metasurface holograms

PubMed Central

Wen, Dandan; Yue, Fuyong; Li, Guixin; Zheng, Guoxing; Chan, Kinlong; Chen, Shumei; Chen, Ming; Li, King Fai; Wong, Polis Wing Han; Cheah, Kok Wai; Yue Bun Pun, Edwin; Zhang, Shuang; Chen, Xianzhong

2015-01-01

Metasurfaces are engineered interfaces that contain a thin layer of plasmonic or dielectric nanostructures capable of manipulating light in a desirable manner. Advances in metasurfaces have led to various practical applications ranging from lensing to holography. Metasurface holograms that can be switched by the polarization state of incident light have been demonstrated for achieving polarization multiplexed functionalities. However, practical application of these devices has been limited by their capability for achieving high efficiency and high image quality. Here we experimentally demonstrate a helicity multiplexed metasurface hologram with high efficiency and good image fidelity over a broad range of frequencies. The metasurface hologram features the combination of two sets of hologram patterns operating with opposite incident helicities. Two symmetrically distributed off-axis images are interchangeable by controlling the helicity of the input light. The demonstrated helicity multiplexed metasurface hologram with its high performance opens avenues for future applications with functionality switchable optical devices. PMID:26354497

Surface-enhanced Raman spectroscopy for the detection of pathogenic DNA and protein in foods

NASA Astrophysics Data System (ADS)

Chowdhury, Mustafa H.; Atkinson, Brad; Good, Theresa; Cote, Gerard L.

2003-07-01

Traditional Raman spectroscopy while extremely sensitive to structure and conformation, is an ineffective tool for the detection of bioanalytes at the sub milimolar level. Surface Enhanced Raman Spectroscopy (SERS) is a technique developed more recently that has been used with applaudable success to enhance the Raman cross-section of a molecule by factors of 106 to 1014. This technique can be exploited in a nanoscale biosensor for the detection of pathogenic proteins and DNA in foods by using a biorecognition molecule to bring a target analyte in close proximity to the mental surface. This is expected to produce a SERS signal of the target analyte, thus making it possible to easily discriminate between the target analyte and possible confounders. In order for the sensor to be effective, the Raman spectra of the target analyte would have to be distinct from that of the biorecognition molecule, as both would be in close proximity to the metal surface and thus be subjected to the SERS effect. In our preliminary studies we have successfully used citrate reduced silver colloidal particles to obtain unique SERS spectra of α-helical and β-sheet bovine serum albumin (BSA) that served as models of an α helical antiobiody (biorecognition element) and a β-sheet target protein (pathogenic prion). In addition, the unique SERS spectra of double stranded and single stranded DNA were also obtained where the single stranded DNA served as the model for the biorecognition element and the double stranded DNA served as themodel for the DNA probe/target hybrid. This provides a confirmation of the feasibility of the method which opens opportunities for potentially wide spread applications in the detection of food pathogens, biowarefare agents, andother bio-analytes.

Low-threshold, nanosecond, high-repetition-rate vortex pulses with controllable helicity generated in Cr,Nd:YAG self-Q-switched microchip laser

NASA Astrophysics Data System (ADS)

He, Hong-Sen; Chen, Zhen; Li, Hong-Bin; Dong, Jun

2018-05-01

A high repetition rate, nanosecond, pulsed optical vortex beam has been generated in a Cr,Nd:YAG self-Q-switched microchip laser pumped by the annular-beam formed with a hollow focus lens. The lasing threshold for vortex pulses is 0.9 W. A pulse width of 6.5 ns and a repetition rate of over 330 kHz have been achieved. The average output power of 1 W and the slope efficiency of 46.6% have been obtained. The helicity of the optical vortices has been controlled by adjusting the tilted angle between Cr,Nd:YAG crystal and output coupler. The work provides a new method for developing pulsed optical vortices for potential applications on quantum communication and optical trapping.

Why double-stranded RNA resists condensation

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

Tolokh, Igor S.; Pabit, Suzette; Katz, Andrea M.

2014-09-15

The addition of small amounts of multivalent cations to solutions containing double-stranded DNA leads to attraction between the negatively charged helices and eventually to condensation. Surprisingly, this effect is suppressed in double-stranded RNA, which carries the same charge as the DNA, but assumes a different double helical form. However, additional characterization of short (25 base-pairs) nucleic acid (NA) duplex structures by circular dichroism shows that measured differences in condensation are not solely determined by duplex helical geometry. Here we combine experiment, theory, and atomistic simulations to propose a mechanism that connects the observed variations in condensation of short NA duplexesmore » with the spatial variation of cobalt hexammine (CoHex) binding at the NA duplex surface. The atomistic picture that emerged showed that CoHex distributions around the NA reveals two major NA-CoHex binding modes -- internal and external -- distinguished by the proximity of bound CoHex to the helical axis. Decreasing trends in experimentally observed condensation propensity of the four studied NA duplexes (from B-like form of homopolymeric DNA, to mixed sequence DNA, to DNA:RNA hybrid, to A-like RNA) are explained by the progressive decrease of a single quantity: the fraction of CoHex ions in the external binding mode. Thus, while NA condensation depends on a complex interplay between various structural and sequence features, our coupled experimental and theoretical results suggest a new model in which a single parameter connects the NA condensation propensity with geometry and sequence dependence of CoHex binding.« less

Zn(II) coordination polymers with flexible V-shaped dicarboxylate ligand: Syntheses, helical structures and properties

NASA Astrophysics Data System (ADS)

Li, Lin; Liu, Chong-Bo; Yang, Gao-Shan; Xiong, Zhi-Qiang; Liu, Hong; Wen, Hui-Liang

2015-11-01

Hydrothermal reactions of 2,2‧-[hexafluoroisopropylidenebis(p-phenyleneoxy)]diacetic acid (H2L) and zinc ions in the presence of N-donor ancillary ligands afford four novel coordination polymers, namely, [Zn2(μ2-OH)(μ4-O)0.5(L)]·0.5H2O (1), [Zn(L)(2,2‧-bipy)(H2O)] (2), [Zn3(L)3(phen)2]·H2O (3) and [Zn2(L)2(4,4‧-bipy)] (4) (2,2‧-bipy=2,2‧-bipyridine; 4,4‧-bipy=4,4‧-bipyridine; phen=1,10-phenanthroline). Their structures have been determined by single-crystal X-ray diffraction analyses, elemental analyses, IR spectra, powder X-ray diffraction (PXRD), and thermogravimetric (TG) analyses. Complex 1 shows a 3-D clover framework consisting of [Zn4(μ4-O)(μ2-OH)2]4+ clusters, and exhibits a novel (3,8)-connected topological net with the Schläfli symbol of {3·4·5}2{34·44·52·66·710·82}, and contains double-stranded and two kinds of meso-helices. 2 displays a helical chain structure, which is further extended via hydrogen bonds into a 3-D supramolecular structure with meso-helix chains. 3 displays a 2-D {44·62} parallelogram structure, which is further extended via hydrogen bonds into a 3-D supramolecular structure with single-stranded helical chains. 4 shows a 2-D {44·62} square structure with left- and right-handed helical chains. Moreover, the luminescent properties of 1-4 have been investigated.

Hydrodynamics of insect spermatozoa

NASA Astrophysics Data System (ADS)

Pak, On Shun; Lauga, Eric

2010-11-01

Microorganism motility plays important roles in many biological processes including reproduction. Many microorganisms propel themselves by propagating traveling waves along their flagella. Depending on the species, propagation of planar waves (e.g. Ceratium) and helical waves (e.g. Trichomonas) were observed in eukaryotic flagellar motion, and hydrodynamic models for both were proposed in the past. However, the motility of insect spermatozoa remains largely unexplored. An interesting morphological feature of such cells, first observed in Tenebrio molitor and Bacillus rossius, is the double helical deformation pattern along the flagella, which is characterized by the presence of two superimposed helical flagellar waves (one with a large amplitude and low frequency, and the other with a small amplitude and high frequency). Here we present the first hydrodynamic investigation of the locomotion of insect spermatozoa. The swimming kinematics, trajectories and hydrodynamic efficiency of the swimmer are computed based on the prescribed double helical deformation pattern. We then compare our theoretical predictions with experimental measurements, and explore the dependence of the swimming performance on the geometric and dynamical parameters.

Why double-stranded RNA resists condensation

PubMed Central

Tolokh, Igor S.; Pabit, Suzette A.; Katz, Andrea M.; Chen, Yujie; Drozdetski, Aleksander; Baker, Nathan; Pollack, Lois; Onufriev, Alexey V.

2014-01-01

The addition of small amounts of multivalent cations to solutions containing double-stranded DNA leads to inter-DNA attraction and eventual condensation. Surprisingly, the condensation is suppressed in double-stranded RNA, which carries the same negative charge as DNA, but assumes a different double helical form. Here, we combine experiment and atomistic simulations to propose a mechanism that explains the variations in condensation of short (25 base-pairs) nucleic acid (NA) duplexes, from B-like form of homopolymeric DNA, to mixed sequence DNA, to DNA:RNA hybrid, to A-like RNA. Circular dichroism measurements suggest that duplex helical geometry is not the fundamental property that ultimately determines the observed differences in condensation. Instead, these differences are governed by the spatial variation of cobalt hexammine (CoHex) binding to NA. There are two major NA-CoHex binding modes—internal and external—distinguished by the proximity of bound CoHex to the helical axis. We find a significant difference, up to 5-fold, in the fraction of ions bound to the external surfaces of the different NA constructs studied. NA condensation propensity is determined by the fraction of CoHex ions in the external binding mode. PMID:25123663

TH-C-18A-11: Investigating the Minimum Scan Parameters Required to Generate Free-Breathing Fast-Helical CT Scans Without Motion-Artifacts

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

Thomas, D; Neylon, J; Dou, T

Purpose: A recently proposed 4D-CT protocol uses deformable registration of free-breathing fast-helical CT scans to generate a breathing motion model. In order to allow accurate registration, free-breathing images are required to be free of doubling-artifacts, which arise when tissue motion is greater than scan speed. This work identifies the minimum scanner parameters required to successfully generate free-breathing fast-helical scans without doubling-artifacts. Methods: 10 patients were imaged under free breathing conditions 25 times in alternating directions with a 64-slice CT scanner using a low dose fast helical protocol. A high temporal resolution (0.1s) 4D-CT was generated using a patient specific motionmore » model and patient breathing waveforms, and used as the input for a scanner simulation. Forward projections were calculated using helical cone-beam geometry (800 projections per rotation) and a GPU accelerated reconstruction algorithm was implemented. Various CT scanner detector widths and rotation times were simulated, and verified using a motion phantom. Doubling-artifacts were quantified in patient images using structural similarity maps to determine the similarity between axial slices. Results: Increasing amounts of doubling-artifacts were observed with increasing rotation times > 0.2s for 16×1mm slice scan geometry. No significant increase in doubling artifacts was observed for 64×1mm slice scan geometry up to 1.0s rotation time although blurring artifacts were observed >0.6s. Using a 16×1mm slice scan geometry, a rotation time of less than 0.3s (53mm/s scan speed) would be required to produce images of similar quality to a 64×1mm slice scan geometry. Conclusion: The current generation of 16 slice CT scanners, which are present in most Radiation Oncology departments, are not capable of generating free-breathing sorting-artifact-free images in the majority of patients. The next generation of CT scanners should be capable of at least 53mm/s scan speed in order to use a fast-helical 4D-CT protocol to generate a motion-artifact free 4D-CT. NIH R01CA096679.« less

Chemotaxis without Conventional Two-Component System, Based on Cell Polarity and Aerobic Conditions in Helicity-Switching Swimming of Spiroplasma eriocheiris

PubMed Central

Liu, Peng; Zheng, Huajun; Meng, Qingguo; Terahara, Natsuho; Gu, Wei; Wang, Shengyue; Zhao, Guoping; Nakane, Daisuke; Wang, Wen; Miyata, Makoto

2017-01-01

Spiroplasma eriocheiris is a pathogen that causes mass mortality in Chinese mitten crab, Eriocheir sinensis. S. eriocheiris causes tremor disease and infects almost all of the artificial breeding crustaceans, resulting in disastrous effects on the aquaculture economy in China. S. eriocheiris is a wall-less helical bacterium, measuring 2.0 to 10.0 μm long, and can swim up to 5 μm per second in a viscous medium without flagella by switching the cell helicity at a kink traveling from the front to the tail. In this study, we showed that S. eriocheiris performs chemotaxis without the conventional two-component system, a system commonly found in bacterial chemotaxis. The chemotaxis of S. eriocheiris was observed more clearly when the cells were cultivated under anaerobic conditions. The cells were polarized as evidenced by a tip structure, swimming in the direction of the tip, and were shown to reverse their swimming direction in response to attractants. Triton X-100 treatment revealed the internal structure, a dumbbell-shaped core in the tip that is connected by a flat ribbon, which traces the shortest line in the helical cell shape from the tip to the other pole. Sixteen proteins were identified as the components of the internal structure by mass spectrometry, including Fibril protein and four types of MreB proteins. PMID:28217108

Extensively Reversible Thermal Transformations of a Bistable, Fluorescence-Switchable Molecular Solid: Entry into Functional Molecular Phase-Change Materials.

PubMed

Srujana, P; Radhakrishnan, T P

2015-06-15

Functional phase-change materials (PCMs) are conspicuously absent among molecular materials in which the various attributes of inorganic solids have been realized. While organic PCMs are primarily limited to thermal storage systems, the amorphous-crystalline transformation of materials like Ge-Sb-Te find use in advanced applications such as information storage. Reversible amorphous-crystalline transformations in molecular solids require a subtle balance between robust supramolecular assembly and flexible structural elements. We report novel diaminodicyanoquinodimethanes that achieve this transformation by interlinked helical assemblies coupled with conformationally flexible alkoxyalkyl chains. They exhibit highly reversible thermal transformations between bistable (crystalline/amorphous) forms, along with a prominent switching of the fluorescence emission energy and intensity. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Impact on molecular organization of amylopectin in starch granules upon annealing.

PubMed

Vamadevan, Varatharajan; Bertoft, Eric; Soldatov, Dmitriy V; Seetharaman, Koushik

2013-10-15

This study investigated the influence of the internal structure of amylopectin on annealing (3h, 24h) of starches from four different types of amylopectin (Bertoft, Koch, & Aman, 2012; Bertoft, Piyachomkwan, Chatakanonda, & Sriroth, 2008). Regardless of the starch source and incubation time, annealing significantly increased the onset gelatinization temperature (To) and narrowed and deepened the amylopectin endotherm. However, the extent of the change in the melting temperature (Tm) and the enthalpy of gelatinization (ΔH) differed among the types. In terms of the To and Tm, starches from type 1 (oat, rye, barley, and waxy barley) showed the most significant response to annealing. The Tm of starches belonging to type 2 (waxy maize, rice, waxy rice, and sago) remained unchanged after 3h of annealing. Type 1 and type 2 starches with the lowest gelatinization temperatures showed the greatest increase in melting temperature after annealing. However, type 3 (tapioca, mung bean, and arrowroot) and type 4 (potato, waxy potato, canna, and yam) starches were not in line with these observations. Instead, starches from type 3 and type 4 showed a pronounced increase in the ΔH. The inter-block chain length (IB-CL) (distance between tightly branched units within a cluster) correlated positively (r=0.93, p<0.01) with the change in enthalpy after 24h of annealing. These data indicate that a short IB-CL affects the optimum registration of double helices within the crystalline lamellae. The relationship between the gelatinization parameters before and after annealing suggests that type 1 and 2 starches might possess a high number of unpacked double helices (type 1>type 2) compared to other types. Longer IB-CLs, which facilitate the parallel packing of splayed double helices, and the lengthening of double helices likely increased the ΔH in type 3 and type 4 starches. It is concluded that annealing can be used as a probe for visualizing the organization of glucan chains (alignment of double helices/degree of perfection) within crystalline lamellae. Copyright © 2013 Elsevier Ltd. All rights reserved.

High-Efficiency Helical Coil Electromagnetic Launcher and High Power Hall-Effect Switch

DTIC Science & Technology

2008-02-29

also given that demonstrate significant launcher performance benefits by super-cooling the armature (i.e., using liquid nitrogen ). 14. ABSTRACT... liquid nitrogen temperatures). A computer model for a magnetically-controlled Hall-effect switch is developed. The model is constructed in the PSpice...of super-cooling is demonstrated with liquid nitrogen cooling and indicates super-cooled EML operation is desirable if cryo-cooling is practical for

Characterization of the geometry and topology of DNA pictured as a discrete collection of atoms

PubMed Central

Olson, Wilma K.

2014-01-01

The structural and physical properties of DNA are closely related to its geometry and topology. The classical mathematical treatment of DNA geometry and topology in terms of ideal smooth space curves was not designed to characterize the spatial arrangements of atoms found in high-resolution and simulated double-helical structures. We present here new and rigorous numerical methods for the rapid and accurate assessment of the geometry and topology of double-helical DNA structures in terms of the constituent atoms. These methods are well designed for large DNA datasets obtained in detailed numerical simulations or determined experimentally at high-resolution. We illustrate the usefulness of our methodology by applying it to the analysis of three canonical double-helical DNA chains, a 65-bp minicircle obtained in recent molecular dynamics simulations, and a crystallographic array of protein-bound DNA duplexes. Although we focus on fully base-paired DNA structures, our methods can be extended to treat the geometry and topology of melted DNA structures as well as to characterize the folding of arbitrary molecules such as RNA and cyclic peptides. PMID:24791158

HIGH ENERGY GASEOUS DISCHARGE DEVICES

DOEpatents

Josephson, V.

1960-02-16

The high-energy electrical discharge device described comprises an envelope, a pair of main discharge electrodes supported in opposition in the envelope, and a metallic shell symmetrically disposed around and spaced from the discharge path between the electrodes. The metallic shell comprises a first element of spaced helical turns of metallic material and a second element of spaced helical turns of methllic material insulatedly supported in superposition outside the first element and with the turns overlapping the gap between the turns of the first element.

Transmit/receive 3-20 GHz 1.2 mW packaged double-pole-16-throw switching matrix for radar-based target detection

NASA Astrophysics Data System (ADS)

Azhari, Afreen; Kuwano, Yuki; Xiao, Xia; Kikkawa, Takamaro

2018-01-01

A 3-20 GHz transmit/receive (T/R) double-pole-16-throw (DP16T) switching matrix has been developed on a printed circuit board (PCB) to control sixteen antennas in a radar-based portable breast-cancer detection system. The DP16T switch consists of four 65 nm CMOS 0.01-20 GHz double-pole-four-throw (DP4T) switches. The proposed switch increase the number of T/R combinations to 224 from the 196 of a conventional switching matrix in order to construct high-resolution images. Using this switch and a 4 × 4 slot antenna array, a 10 × 10 mm2 aluminum target was detected with an 8-GHz-center-frequency Gaussian monocycle pulse. The power consumption of the switch is only 1.2 mW. To the best of the authors’ knowledge, this is the first T/R radio frequency (RF) DP16T switching matrix, which was realized with four CMOS DP4T switches on a PCB and was measured with RF PCB connectors.

Period doubling induced by thermal noise amplification in genetic circuits

PubMed Central

Ruocco, G.; Fratalocchi, A.

2014-01-01

Rhythms of life are dictated by oscillations, which take place in a wide rage of biological scales. In bacteria, for example, oscillations have been proven to control many fundamental processes, ranging from gene expression to cell divisions. In genetic circuits, oscillations originate from elemental block such as autorepressors and toggle switches, which produce robust and noise-free cycles with well defined frequency. In some circumstances, the oscillation period of biological functions may double, thus generating bistable behaviors whose ultimate origin is at the basis of intense investigations. Motivated by brain studies, we here study an “elemental” genetic circuit, where a simple nonlinear process interacts with a noisy environment. In the proposed system, nonlinearity naturally arises from the mechanism of cooperative stability, which regulates the concentration of a protein produced during a transcription process. In this elemental model, bistability results from the coherent amplification of environmental fluctuations due to a stochastic resonance of nonlinear origin. This suggests that the period doubling observed in many biological functions might result from the intrinsic interplay between nonlinearity and thermal noise. PMID:25404210

Bacterial actin homolog ParM: arguments for an apolar, antiparallel double helix.

PubMed

Erickson, Harold P

2012-09-28

The bacterial actin homolog ParM has always been modeled as a polar filament, comprising two parallel helical strands, like actin itself. I present arguments here that ParM may be an apolar filament, in which the two helical strands are antiparallel. Copyright © 2012 Elsevier Ltd. All rights reserved.

Unraveling double stranded alpha-helical coiled coils: an x-ray diffraction study on hard alpha-keratin fibers.

PubMed

Kreplak, L; Doucet, J; Briki, F

2001-04-15

Transformations of proteins secondary and tertiary structures are generally studied in globular proteins in solution. In fibrous proteins, such as hard alpha-keratin, that contain long and well-defined double stranded alpha-helical coiled coil domains, such study can be directly done on the native fibrous tissue. In order to assess the structural behavior of the coiled coil domains under an axial mechanical stress, wide angle x-ray scattering and small angle x-ray scattering experiments have been carried out on stretched horse hair fibers at relative humidity around 30%. Our observations of the three major axial spacings as a function of the applied macroscopic strain have shown two rates. Up to 4% macroscopic strain the coiled coils were slightly distorted but retained their overall conformation. Above 4% the proportion of coiled coil domains progressively decreased. The main and new result of our study is the observation of the transition from alpha-helical coiled coils to disordered chains instead of the alpha-helical coiled coil to beta-sheet transition that occurs in wet fibers.

6,6″-Dimethyl-2,2':6',2″-terpyridine revisited: new fluorescent silver(I) helicates with in vitro antiproliferative activity via selective nucleoli targeting.

PubMed

Fik, Marta A; Gorczyński, Adam; Kubicki, Maciej; Hnatejko, Zbigniew; Fedoruk-Wyszomirska, Agnieszka; Wyszko, Eliza; Giel-Pietraszuk, Małgorzata; Patroniak, Violetta

2014-10-30

6,6″-Dimethyl-2,2':6',2″-terpyridine ligand (L) reacts in equimolar ratio with Ag(I) ions what results in formation of dinuclear double helicates, which differ in terms of framework and complexity in accordance to counterions and solvent applied. Obtained complexes were thoroughly studied in terms of their biological activity, with the positive antiproliferative outcome on three human cancer cell lines: human breast cancer (T47D), human cervical carcinoma (HeLa) and human lung cancer (A-549). Performed DNA binding experiments showed that given Ag(I) species specifically interact with DNA double helix via intercalation and were visualized by confocal microscopy to specifically bind to the nuclei. All newly synthesized helical systems exhibit promising antimicrobial activity against Gram-negative Escherichia coli and Gram-positive Staphylococcus aureus bacterial strains. Spectrophotometric properties were described as fulfilment of structural studies of newly presented complexes confirming their helical structure in solution. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

High-temperature brushless DC motor controller

DOEpatents

Cieslewski, Crzegorz; Lindblom, Scott C.; Maldonado, Frank J.; Eckert, Michael Nathan

2017-05-16

A motor control system for deployment in high temperature environments includes a controller; a first half-bridge circuit that includes a first high-side switching element and a first low-side switching element; a second half-bridge circuit that includes a second high-side switching element and a second low-side switching element; and a third half-bridge circuit that includes a third high-side switching element and a third; low-side switching element. The motor controller is arranged to apply a pulse width modulation (PWM) scheme to switch the first half-bridge circuit, second half-bridge circuit, and third half-bridge circuit to power a motor.

Model independent new physics analysis in Λ _b→ Λ μ ^+μ ^- decay

NASA Astrophysics Data System (ADS)

Das, Diganta

2018-03-01

We study the rare Λ _b→ Λ μ ^+μ ^- decay in the Standard Model and beyond. Beyond the Standard Model we include new vector and axial-vector operators, scalar and pseudo-scalar operators, and tensor operators in the effective Hamiltonian. Working in the helicity basis and using appropriate parametrization of the Λ _b → Λ hadronic matrix elements, we give expressions of hadronic and leptonic helicity amplitudes and derive expression of double differential branching ratio with respect to dilepton invariant mass squared and cosine of lepton angle. Appropriately integrating the differential branching ratio over the lepton angle, we obtain the longitudinal polarization fraction and the leptonic forward-backward asymmetry and sequentially study the observables in the presence of the new couplings. To analyze the implications of the new vector and axial-vector couplings, we follow the current global fits to b→ sμ ^+μ ^- data. While the impacts of scalar couplings can be significant, exclusive \\bar{B}→ X_sμ ^+μ ^- data imply stringent constraints on the tensor couplings and hence the effects on Λ _b→ Λ μ ^+μ ^- are negligible.

Overview of the Helicity Injected Torus (HIT) Program

NASA Astrophysics Data System (ADS)

Redd, A. J.; Jarboe, T. R.; Hamp, W. T.; Nelson, B. A.; O'Neill, R. G.; Sieck, P. E.; Smith, R. J.; Sutphin, G. L.; Wrobel, J. S.

2007-06-01

The Helicity Injected Torus with Steady Inductive Helicity Injection (HIT-SI) consists of a "bowtie"-shaped axisymmetric confinement region, with two half-torus helicity injectors mounted on each side of the axisymmetric flux conserver [Sieck et al, IEEE Trans. Plasma Sci., v.33, p.723 (2005); Jarboe, Fusion Technology, v.36, p.85 (1999)]. Current and flux are driven sinusoidally with time in each injector, with the goal of generating and sustaining an axisymmetric spheromak in the main confinement region. Improvements in machine conditioning have enabled systematic study of HIT-SI discharges with significant toroidal current ITOR, including cases in which this current ITOR switches sign one or more times during the discharge. Statistical studies of all HIT-SI discharges to date demonstrate a minimum injected power to form significant ITOR, and that the maximum ITOR scales approximately linearly with the total injected power.

Engineered materials for all-optical helicity-dependent magnetic switching

NASA Astrophysics Data System (ADS)

Mangin, S.; Gottwald, M.; Lambert, C.-H.; Steil, D.; Uhlíř, V.; Pang, L.; Hehn, M.; Alebrand, S.; Cinchetti, M.; Malinowski, G.; Fainman, Y.; Aeschlimann, M.; Fullerton, E. E.

2014-03-01

The possibility of manipulating magnetic systems without applied magnetic fields have attracted growing attention over the past fifteen years. The low-power manipulation of the magnetization, preferably at ultrashort timescales, has become a fundamental challenge with implications for future magnetic information memory and storage technologies. Here we explore the optical manipulation of the magnetization in engineered magnetic materials. We demonstrate that all-optical helicity-dependent switching (AO-HDS) can be observed not only in selected rare earth-transition metal (RE-TM) alloy films but also in a much broader variety of materials, including RE-TM alloys, multilayers and heterostructures. We further show that RE-free Co-Ir-based synthetic ferrimagnetic heterostructures designed to mimic the magnetic properties of RE-TM alloys also exhibit AO-HDS. These results challenge present theories of AO-HDS and provide a pathway to engineering materials for future applications based on all-optical control of magnetic order.

The structure and dynamics in solution of Cu(I) pseudoazurin from Paracoccus pantotrophus.

PubMed Central

Thompson, G. S.; Leung, Y. C.; Ferguson, S. J.; Radford, S. E.; Redfield, C.

2000-01-01

The solution structure and backbone dynamics of Cu(I) pseudoazurin, a 123 amino acid electron transfer protein from Paracoccus pantotrophus, have been determined using NMR methods. The structure was calculated to high precision, with a backbone RMS deviation for secondary structure elements of 0.35+/-0.06 A, using 1,498 distance and 55 torsion angle constraints. The protein has a double-wound Greek-key fold with two alpha-helices toward its C-terminus, similar to that of its oxidized counterpart determined by X-ray crystallography. Comparison of the Cu(I) solution structure with the X-ray structure of the Cu(II) protein shows only small differences in the positions of some of the secondary structure elements. Order parameters S2, measured for amide nitrogens, indicate that the backbone of the protein is rigid on the picosecond to nanosecond timescale. PMID:10850794

Inductance Calculations of Variable Pitch Helical Inductors

DTIC Science & Technology

2015-08-01

8217 ’ Integral solution using Simpson’s Rule ’ Dim i As Integer Dim Pi As Double, uo As Double, kc As Double Dim a As Double, amax As Double, da As...Double Dim steps As Integer Dim func1a As Double, func1b As Double ’ On Error GoTo err_TorisV1 steps = 1000 Pi = 3.14159 uo = 4 * Pi * 0.0000001...As Double ’ ’ Integral solution using Simpson’s Rule ’ Dim i As Integer Dim Pi As Double, uo As Double, kc As Double Dim a As Double, amax As

Double Current Sheet Instabilities and the Transition to Turbulence.

NASA Astrophysics Data System (ADS)

Pucci, F.; Velli, M.; Biferale, L.; Sahoo, G.

2016-12-01

The double tearing instability has often been studied as a proxy for the m=1 kink mode in cylindrical plasma. In this paper we describe the results of 3D simulations of an initially periodic double current sheet described by Harris equilibria with a guide field in two cases: 1) zero net helicity and an average magnetic field and 2) a well defined helicity (force free but non constant alpha). We study and contrast the de-stabilization and transition to turbulence for these two cases: we describe spectra, cascades, and possible application to heliospheric phenomena, in particular CME evolution and relaxation. The research leading to these results has received fund- ing from the European Union's Seventh Framework Pro- gramme (FP7/2007-2013) under grant agreement No. 339032

Critical switching fluence of L10-FePt nanoparticles with practical size to ultrafast all-optical polarization switching

NASA Astrophysics Data System (ADS)

Huang, Tao; Wang, Haiwei; Cheng, Weiming; Zou, Yuhao; Xie, Changsheng

2017-06-01

The magnetic storage industry will be pushed into a new era by emerging magnetic materials and ingenious read/write techniques. Recently, L10-FePt nanoparticles with exceptionally high uniaxial anisotropy, combined with the technique of all-optical magnetic switching, have increasingly drawn the attention of researchers. Focusing on L10-FePt nanoparticles, we report the superparamagnetic size limits and three elaborate stages of magnetic orientation switching, which demonstrate that in terms of the opto-magnetic responses of L10-FePt nanoparticles with the size of 6 nm, the fluence of an ultrashort laser pulse should not be larger than the level of 40 mJ/cm2 in order to achieve the helicity-dependent all-optical switching.

A Double-Pole High Voltage High Current Switch

DTIC Science & Technology

2005-12-01

NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS Approved for public release; distribution is unlimited A DOUBLE- POLE HIGH...December 2005 3. REPORT TYPE AND DATES COVERED Master’s Thesis 4. TITLE AND SUBTITLE: A Double- Pole High Voltage High Current Switch 6. AUTHOR(S...to divert heavy charged particles, e.g. Cu+. 15. NUMBER OF PAGES 68 14. SUBJECT TERMS Double- Pole , Pulse Forming Inductive Network, PFIN

Fast helicity switching of x-ray circular polarization at beamline P09 at PETRA III

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

Strempfer, J., E-mail: Joerg.Strempfer@desy.de; Mardegan, J. R. L.; Francoual, S.

At the resonant scattering and diffraction beamline P09 at PETRA III/DESY, polarization manipulation in the X-ray energy range 3-13 keV is possible using wave-plates. Recently, fast flipping of circular polarization helicity using the Raspberry Pi controlled FPGA (PiLC) device developed at DESY and dedicated piezo-electric flippers has been commissioned. Functionality of the PiLC for XMCD and first XMCD measurements at the Fe K-and Dy-L{sub 3} absorption edges are presented.

Template switching between PNA and RNA oligonucleotides

NASA Technical Reports Server (NTRS)

Bohler, C.; Nielsen, P. E.; Orgel, L. E.; Miller, S. L. (Principal Investigator)

1995-01-01

The origin of the RNA world is not easily understood, as effective prebiotic syntheses of the components of RNA, the beta-ribofuranoside-5'-phosphates, are hard to envisage. Recognition of this difficulty has led to the proposal that other genetic systems, the components of which are more easily formed, may have preceded RNA. This raises the question of how transitions between one genetic system and another could occur. Peptide nucleic acid (PNA) resembles RNA in its ability to form double-helical complexes stabilized by Watson-Crick hydrogen bonding between adenine and thymine and between cytosine and guanine, but has a backbone that is held together by amide rather than by phosphodiester bonds. Oligonucleotides bases on RNA are known to act as templates that catalyse the non-enzymatic synthesis of their complements from activated mononucleotides, we now show that RNA oligonucleotides facilitate the synthesis of complementary PNA strands and vice versa. This suggests that a transition between different genetic systems can occur without loss of information.

Coupled multiferroic domain switching in the canted conical spin spiral system Mn2GeO4

NASA Astrophysics Data System (ADS)

Honda, T.; White, J. S.; Harris, A. B.; Chapon, L. C.; Fennell, A.; Roessli, B.; Zaharko, O.; Murakami, Y.; Kenzelmann, M.; Kimura, T.

2017-06-01

Despite remarkable progress in developing multifunctional materials, spin-driven ferroelectrics featuring both spontaneous magnetization and electric polarization are still rare. Among such ferromagnetic ferroelectrics are conical spin spiral magnets with a simultaneous reversal of magnetization and electric polarization that is still little understood. Such materials can feature various multiferroic domains that complicates their study. Here we study the multiferroic domains in ferromagnetic ferroelectric Mn2GeO4 using neutron diffraction, and show that it features a double-Q conical magnetic structure that, apart from trivial 180o commensurate magnetic domains, can be described by ferromagnetic and ferroelectric domains only. We show unconventional magnetoelectric couplings such as the magnetic-field-driven reversal of ferroelectric polarization with no change of spin-helicity, and present a phenomenological theory that successfully explains the magnetoelectric coupling. Our measurements establish Mn2GeO4 as a conceptually simple multiferroic in which the magnetic-field-driven flop of conical spin spirals leads to the simultaneous reversal of magnetization and electric polarization.

Optimized two-color super resolution imaging of Drp1 during mitochondrial fission with a slow-switching Dronpa variant.

PubMed

Rosenbloom, Alyssa B; Lee, Sang-Hyuk; To, Milton; Lee, Antony; Shin, Jae Yen; Bustamante, Carlos

2014-09-09

We studied the single-molecule photo-switching properties of Dronpa, a green photo-switchable fluorescent protein and a popular marker for photoactivated localization microscopy. We found the excitation light photoactivates as well as deactivates Dronpa single molecules, hindering temporal separation and limiting super resolution. To resolve this limitation, we have developed a slow-switching Dronpa variant, rsKame, featuring a V157L amino acid substitution proximal to the chromophore. The increased steric hindrance generated by the substitution reduced the excitation light-induced photoactivation from the dark to fluorescent state. To demonstrate applicability, we paired rsKame with PAmCherry1 in a two-color photoactivated localization microscopy imaging method to observe the inner and outer mitochondrial membrane structures and selectively labeled dynamin related protein 1 (Drp1), responsible for membrane scission during mitochondrial fission. We determined the diameter and length of Drp1 helical rings encircling mitochondria during fission and showed that, whereas their lengths along mitochondria were not significantly changed, their diameters decreased significantly. These results suggest support for the twistase model of Drp1 constriction, with potential loss of subunits at the helical ends.

On-board processing satellite network architecture and control study

NASA Technical Reports Server (NTRS)

Campanella, S. Joseph; Pontano, Benjamin A.; Chalmers, Harvey

1987-01-01

The market for telecommunications services needs to be segmented into user classes having similar transmission requirements and hence similar network architectures. Use of the following transmission architecture was considered: satellite switched TDMA; TDMA up, TDM down; scanning (hopping) beam TDMA; FDMA up, TDM down; satellite switched MF/TDMA; and switching Hub earth stations with double hop transmission. A candidate network architecture will be selected that: comprises multiple access subnetworks optimized for each user; interconnects the subnetworks by means of a baseband processor; and optimizes the marriage of interconnection and access techniques. An overall network control architecture will be provided that will serve the needs of the baseband and satellite switched RF interconnected subnetworks. The results of the studies shall be used to identify elements of network architecture and control that require the greatest degree of technology development to realize an operational system. This will be specified in terms of: requirements of the enabling technology; difference from the current available technology; and estimate of the development requirements needed to achieve an operational system. The results obtained for each of these tasks are presented.

Dual-gate GaAs FET switches

NASA Astrophysics Data System (ADS)

Vorhaus, J. L.; Fabian, W.; Ng, P. B.; Tajima, Y.

1981-02-01

A set of multi-pole, multi-throw switch devices consisting of dual-gate GaAs FET's is described. Included are single-pole, single-throw (SPST), double-pole, double-throw (DPDT), and single-pole four-throw (SP4T) switches. Device fabrication and measurement techniques are discussed. The device models for these switches were based on an equivalent circuit of a dual-gate FET. The devices were found to have substantial gain in X-band and low Ku-band.

Topological switching between an alpha-beta parallel protein and a remarkably helical molten globule.

PubMed

Nabuurs, Sanne M; Westphal, Adrie H; aan den Toorn, Marije; Lindhoud, Simon; van Mierlo, Carlo P M

2009-06-17

Partially folded protein species transiently exist during folding of most proteins. Often these species are molten globules, which may be on- or off-pathway to native protein. Molten globules have a substantial amount of secondary structure but lack virtually all the tertiary side-chain packing characteristic of natively folded proteins. These ensembles of interconverting conformers are prone to aggregation and potentially play a role in numerous devastating pathologies, and thus attract considerable attention. The molten globule that is observed during folding of apoflavodoxin from Azotobacter vinelandii is off-pathway, as it has to unfold before native protein can be formed. Here we report that this species can be trapped under nativelike conditions by substituting amino acid residue F44 by Y44, allowing spectroscopic characterization of its conformation. Whereas native apoflavodoxin contains a parallel beta-sheet surrounded by alpha-helices (i.e., the flavodoxin-like or alpha-beta parallel topology), it is shown that the molten globule has a totally different topology: it is helical and contains no beta-sheet. The presence of this remarkably nonnative species shows that single polypeptide sequences can code for distinct folds that swap upon changing conditions. Topological switching between unrelated protein structures is likely a general phenomenon in the protein structure universe.

Fabrication of chiroptically switchable films via co-gelation of a small chiral gelator with an achiral azobenzene-containing polymer.

PubMed

Yang, Dong; Zhang, Li; Yin, Lu; Zhao, Yin; Zhang, Wei; Liu, Minghua

2017-09-20

Helical polymers are widely found in nature and synthetic functional materials. Although a number of elaborate strategies have been developed to endow polymers with helicity through either covalent bonds or supramolecular techniques, it still remains a challenge to get the desired helical polymers with controlled handedness in an easy but effective manner. In this study, we report an easily accessible gelation-guided self-assembly system where the chirality of a gelator can be easily transferred to an achiral azobenzene-containing polymer during gelation. It is found that during the process of chiral induction, the induced chirality of the polymer was entirely dominated by the molecular chirality of the gelator. Experimentally, achiral azobenzene-containing polymers with different side-chain lengths were doped into a supramolecular gel system formed with amphiphilic N,N'-bis-(octadecyl)-l(d)-Boc-glutamic (LBG-18 or DBG-18 for short). CD spectra and SEM observation confirmed that the co-assembly of polymer/LBG-18 or polymer/DBG-18 in the xerogel state exhibited supramolecular chirality. More importantly, alternate UV and visible light irradiation on the xerogel film caused the induced CD signal to switch between on and off states. Thus a chiroptical switch was fabricated based on the isomerization of the azo-polymer in xerogel films.

Non-volatile, solid state bistable electrical switch

NASA Technical Reports Server (NTRS)

Williams, Roger M. (Inventor)

1994-01-01

A bistable switching element is made of a material whose electrical resistance reversibly decreases in response to intercalation by positive ions. Flow of positive ions between the bistable switching element and a positive ion source is controlled by means of an electrical potential applied across a thermal switching element. The material of the thermal switching element generates heat in response to electrical current flow therethrough, which in turn causes the material to undergo a thermal phase transition from a high electrical resistance state to a low electrical resistance state as the temperature increases above a predetermined value. Application of the electrical potential in one direction renders the thermal switching element conductive to pass electron current out of the ion source. This causes positive ions to flow from the source into the bistable switching element and intercalate the same to produce a non-volatile, low resistance logic state. Application of the electrical potential in the opposite direction causes reverse current flow which de-intercalates the bistable logic switching element and produces a high resistance logic state.

Design and construction of a double inversion recombination switch for heritable sequential genetic memory.

PubMed

Ham, Timothy S; Lee, Sung K; Keasling, Jay D; Arkin, Adam P

2008-07-30

Inversion recombination elements present unique opportunities for computing and information encoding in biological systems. They provide distinct binary states that are encoded into the DNA sequence itself, allowing us to overcome limitations posed by other biological memory or logic gate systems. Further, it is in theory possible to create complex sequential logics by careful positioning of recombinase recognition sites in the sequence. In this work, we describe the design and synthesis of an inversion switch using the fim and hin inversion recombination systems to create a heritable sequential memory switch. We have integrated the two inversion systems in an overlapping manner, creating a switch that can have multiple states. The switch is capable of transitioning from state to state in a manner analogous to a finite state machine, while encoding the state information into DNA. This switch does not require protein expression to maintain its state, and "remembers" its state even upon cell death. We were able to demonstrate transition into three out of the five possible states showing the feasibility of such a switch. We demonstrate that a heritable memory system that encodes its state into DNA is possible, and that inversion recombination system could be a starting point for more complex memory circuits. Although the circuit did not fully behave as expected, we showed that a multi-state, temporal memory is achievable.

Design and Construction of a Double Inversion Recombination Switch for Heritable Sequential Genetic Memory

PubMed Central

Ham, Timothy S.; Lee, Sung K.; Keasling, Jay D.; Arkin, Adam P.

2008-01-01

Background Inversion recombination elements present unique opportunities for computing and information encoding in biological systems. They provide distinct binary states that are encoded into the DNA sequence itself, allowing us to overcome limitations posed by other biological memory or logic gate systems. Further, it is in theory possible to create complex sequential logics by careful positioning of recombinase recognition sites in the sequence. Methodology/Principal Findings In this work, we describe the design and synthesis of an inversion switch using the fim and hin inversion recombination systems to create a heritable sequential memory switch. We have integrated the two inversion systems in an overlapping manner, creating a switch that can have multiple states. The switch is capable of transitioning from state to state in a manner analogous to a finite state machine, while encoding the state information into DNA. This switch does not require protein expression to maintain its state, and “remembers” its state even upon cell death. We were able to demonstrate transition into three out of the five possible states showing the feasibility of such a switch. Conclusions/Significance We demonstrate that a heritable memory system that encodes its state into DNA is possible, and that inversion recombination system could be a starting point for more complex memory circuits. Although the circuit did not fully behave as expected, we showed that a multi-state, temporal memory is achievable. PMID:18665232

Three-dimensional quantification of vorticity and helicity from 3D cine PC-MRI using finite-element interpolations.

PubMed

Sotelo, Julio; Urbina, Jesús; Valverde, Israel; Mura, Joaquín; Tejos, Cristián; Irarrazaval, Pablo; Andia, Marcelo E; Hurtado, Daniel E; Uribe, Sergio

2018-01-01

We propose a 3D finite-element method for the quantification of vorticity and helicity density from 3D cine phase-contrast (PC) MRI. By using a 3D finite-element method, we seamlessly estimate velocity gradients in 3D. The robustness and convergence were analyzed using a combined Poiseuille and Lamb-Ossen equation. A computational fluid dynamics simulation was used to compared our method with others available in the literature. Additionally, we computed 3D maps for different 3D cine PC-MRI data sets: phantom without and with coarctation (18 healthy volunteers and 3 patients). We found a good agreement between our method and both the analytical solution of the combined Poiseuille and Lamb-Ossen. The computational fluid dynamics results showed that our method outperforms current approaches to estimate vorticity and helicity values. In the in silico model, we observed that for a tetrahedral element of 2 mm of characteristic length, we underestimated the vorticity in less than 5% with respect to the analytical solution. In patients, we found higher values of helicity density in comparison to healthy volunteers, associated with vortices in the lumen of the vessels. We proposed a novel method that provides entire 3D vorticity and helicity density maps, avoiding the used of reformatted 2D planes from 3D cine PC-MRI. Magn Reson Med 79:541-553, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Topological Material-Based Spin Devices

NASA Astrophysics Data System (ADS)

Zhang, Minhao; Wang, Xuefeng

Three-dimensional topological insulators have insulating bulk and gapless helical surface states. One of the most fascinating properties of the metallic surface states is the spin-momentum helical locking. The giant current-driven torques on the magnetic layer have been discovered in TI/ferromagnet bilayers originating from the spin-momentum helical locking, enabling the efficient magnetization switching with a low current density. We demonstrated the current-direction dependent on-off state in TIs-based spin valve devices for memory and logic applications. Further, we demonstrated the Bi2Se3 system will go from a topologically nontrivial state to a topologically trivial state when Bi atoms are replaced by lighter In atoms. Here, topologically trivial metal (BixIny)2 Se3 with high mobility also facilitates the realization of its application in multifunctional spintronic devices.

Zn(II) coordination polymers with flexible V-shaped dicarboxylate ligand: Syntheses, helical structures and properties

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

Li, Lin; Liu, Chong-Bo, E-mail: cbliu@nchu.edu.cn; Yang, Gao-Shan

2015-11-15

Hydrothermal reactions of 2,2′-[hexafluoroisopropylidenebis(p-phenyleneoxy)]diacetic acid (H{sub 2}L) and zinc ions in the presence of N-donor ancillary ligands afford four novel coordination polymers, namely, [Zn{sub 2}(μ{sub 2}-OH)(μ{sub 4}-O){sub 0.5}(L)]·0.5H{sub 2}O (1), [Zn(L)(2,2′-bipy)(H{sub 2}O)] (2), [Zn{sub 3}(L){sub 3}(phen){sub 2}]·H{sub 2}O (3) and [Zn{sub 2}(L){sub 2}(4,4′-bipy)] (4) (2,2′-bipy=2,2′-bipyridine; 4,4′-bipy=4,4′-bipyridine; phen=1,10-phenanthroline). Their structures have been determined by single-crystal X-ray diffraction analyses, elemental analyses, IR spectra, powder X-ray diffraction (PXRD), and thermogravimetric (TG) analyses. Complex 1 shows a 3-D clover framework consisting of [Zn{sub 4}(µ{sub 4}-O)(µ{sub 2}-OH){sub 2}]{sup 4+} clusters, and exhibits a novel (3,8)-connected topological net with the Schläfli symbol of {3·4·5}{sub 2}{3"4·4"4·5"2·6"6·7"1"0·8"2}, andmore » contains double-stranded and two kinds of meso-helices. 2 displays a helical chain structure, which is further extended via hydrogen bonds into a 3-D supramolecular structure with meso-helix chains. 3 displays a 2-D {4"4·6"2} parallelogram structure, which is further extended via hydrogen bonds into a 3-D supramolecular structure with single-stranded helical chains. 4 shows a 2-D {4"4·6"2} square structure with left- and right-handed helical chains. Moreover, the luminescent properties of 1–4 have been investigated. - Graphical abstract: Four new Zn(II) coordination polymers with helical structures based on flexible V-shaped dicarboxylate ligand have been synthesized and structurally characterized. Photoluminescent properties have been investigated. - Highlights: • Four novel Zn(II) coordination polymers with V-shaped ligand were characterized. • Complexes 1–4 show diverse intriguing helical characters. • Fluorescence properties of complexes 1–4 were investigated.« less

High Efficiency Single Output ZVS-ZCS Voltage Doubled Flyback Converter

NASA Astrophysics Data System (ADS)

Kaliyaperumal, Deepa; Saju, Hridya Merin; Kumar, M. Vijaya

2016-06-01

A switch operating at high switching frequency increases the switching losses of the converter resulting in lesser efficiency. Hence this paper proposes a new topology which has resonant switches [zero voltage switching (ZVS)] in the primary circuit to eliminate the above said disadvantages, and voltage doubler zero current switching (ZCS) circuit in the secondary to double the output voltage, and hence the output power, power density and efficiency. The design aspects of the proposed topology for a single output of 5 V at 50 kHz, its simulation and hardware results are discussed in detail. The analysis of the results obtained from a 2.5 W converter reveals the superiority of the proposed converter.

Peptide tessellation yields micrometre-scale collagen triple helices

NASA Astrophysics Data System (ADS)

Tanrikulu, I. Caglar; Forticaux, Audrey; Jin, Song; Raines, Ronald T.

2016-11-01

Sticky-ended DNA duplexes can associate spontaneously into long double helices; however, such self-assembly is much less developed with proteins. Collagen is the most prevalent component of the extracellular matrix and a common clinical biomaterial. As for natural DNA, the ~103-residue triple helices (~300 nm) of natural collagen are recalcitrant to chemical synthesis. Here we show how the self-assembly of short collagen-mimetic peptides (CMPs) can enable the fabrication of synthetic collagen triple helices that are nearly a micrometre in length. Inspired by the mathematics of tessellations, we derive rules for the design of single CMPs that self-assemble into long triple helices with perfect symmetry. Sticky ends thus created are uniform across the assembly and drive its growth. Enacting this design yields individual triple helices that, in length, match or exceed those in natural collagen and are remarkably thermostable, despite the absence of higher-order association. The symmetric assembly of CMPs provides an enabling platform for the development of advanced materials for medicine and nanotechnology.

Computer-Aided Design of RNA Origami Structures.

PubMed

Sparvath, Steffen L; Geary, Cody W; Andersen, Ebbe S

2017-01-01

RNA nanostructures can be used as scaffolds to organize, combine, and control molecular functionalities, with great potential for applications in nanomedicine and synthetic biology. The single-stranded RNA origami method allows RNA nanostructures to be folded as they are transcribed by the RNA polymerase. RNA origami structures provide a stable framework that can be decorated with functional RNA elements such as riboswitches, ribozymes, interaction sites, and aptamers for binding small molecules or protein targets. The rich library of RNA structural and functional elements combined with the possibility to attach proteins through aptamer-based binding creates virtually limitless possibilities for constructing advanced RNA-based nanodevices.In this chapter we provide a detailed protocol for the single-stranded RNA origami design method using a simple 2-helix tall structure as an example. The first step involves 3D modeling of a double-crossover between two RNA double helices, followed by decoration with tertiary motifs. The second step deals with the construction of a 2D blueprint describing the secondary structure and sequence constraints that serves as the input for computer programs. In the third step, computer programs are used to design RNA sequences that are compatible with the structure, and the resulting outputs are evaluated and converted into DNA sequences to order.

Two new families of high-gain dc-dc power electronic converters for dc-microgrids

NASA Astrophysics Data System (ADS)

Prabhala, Venkata Anand Kishore

Distributing the electric power in dc form is an appealing solution in many applications such as telecommunications, data centers, commercial buildings, and microgrids. A high gain dc-dc power electronic converter can be used to individually link low-voltage elements such as solar panels, fuel cells, and batteries to the dc voltage bus which is usually 400 volts. This way, it is not required to put such elements in a series string to build up their voltages. Consequently, each element can function at it optimal operating point regardless of the other elements in the system. In this dissertation, first a comparative study of dc microgrid architectures and their advantages over their ac counterparts is presented. Voltage level selection of dc distribution systems is discussed from the cost, reliability, efficiency, and safety standpoints. Next, a new family of non-isolated high-voltage-gain dc-dc power electronic converters with unidirectional power flow is introduced. This family of converters benefits from a low voltage stress across its switches. The proposed topologies are versatile as they can be utilized as single-input or double-input power converters. In either case, they draw continuous currents from their sources. Lastly, a bidirectional high-voltage-gain dc-dc power electronic converter is proposed. This converter is comprised of a bidirectional boost converter which feeds a switched-capacitor architecture. The switched-capacitor stage suggested here has several advantages over the existing approaches. For example, it benefits from a higher voltage gain while it uses less number of capacitors. The proposed converters are highly efficient and modular. The operating modes, dc voltage gain, and design procedure for each converter are discussed in details. Hardware prototypes have been developed in the lab. The results obtained from the hardware agree with those of the simulation models.

Task switching in a hierarchical task structure: evidence for the fragility of the task repetition benefit.

PubMed

Lien, Mei-Ching; Ruthruff, Eric

2004-05-01

This study examined how task switching is affected by hierarchical task organization. Traditional task-switching studies, which use a constant temporal and spatial distance between each task element (defined as a stimulus requiring a response), promote a flat task structure. Using this approach, Experiment 1 revealed a large switch cost of 238 ms. In Experiments 2-5, adjacent task elements were grouped temporally and/or spatially (forming an ensemble) to create a hierarchical task organization. Results indicate that the effect of switching at the ensemble level dominated the effect of switching at the element level. Experiments 6 and 7, using an ensemble of 3 task elements, revealed that the element-level switch cost was virtually absent between ensembles but was large within an ensemble. The authors conclude that the element-level task repetition benefit is fragile and can be eliminated in a hierarchical task organization.

Task switching in a hierarchical task structure: evidence for the fragility of the task repetition benefit

NASA Technical Reports Server (NTRS)

Lien, Mei-Ching; Ruthruff, Eric

2004-01-01

This study examined how task switching is affected by hierarchical task organization. Traditional task-switching studies, which use a constant temporal and spatial distance between each task element (defined as a stimulus requiring a response), promote a flat task structure. Using this approach, Experiment 1 revealed a large switch cost of 238 ms. In Experiments 2-5, adjacent task elements were grouped temporally and/or spatially (forming an ensemble) to create a hierarchical task organization. Results indicate that the effect of switching at the ensemble level dominated the effect of switching at the element level. Experiments 6 and 7, using an ensemble of 3 task elements, revealed that the element-level switch cost was virtually absent between ensembles but was large within an ensemble. The authors conclude that the element-level task repetition benefit is fragile and can be eliminated in a hierarchical task organization.

Folding control in cyclic peptides through N-methylation pattern selection: formation of antiparallel beta-sheet dimers, double reverse turns and supramolecular helices by 3alpha,gamma cyclic peptides.

PubMed

Amorín, Manuel; Castedo, Luis; Granja, Juan R

2008-01-01

Peptide foldamers constitute a growing class of nanomaterials with potential applications in a wide variety of chemical, medical and technological fields. Here we describe the preparation and structural characteristics of a new class of cyclic peptide foldamers (3alpha,gamma-CPs) that, depending on their backbone N-methylation patterns and the medium, can either remain as flat rings that dimerize through arrays of hydrogen bonds of antiparallel beta-sheet type, or can fold into twisted double reverse turns that, in the case of double gamma-turns, associate in nonpolar solvents to form helical supramolecular structures. A 3alpha,gamma-CP consists of a number of multiples of a repeat unit made up of four amino acid residues of alternating chirality: three corresponding to alpha-amino acids and one to a gamma-amino acid (a cis-3-aminocycloalkanecarboxylic acid).

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

Kundu, Sourav, E-mail: sourav.kundu@saha.ac.in; Karmakar, S. N., E-mail: sachindranath.karmakar@saha.ac.in

We present a tight-binding study of conformation dependent electronic transport properties of DNA double-helix including its helical symmetry. We have studied the changes in the localization properties of DNA as we alter the number of stacked bases within every pitch of the double-helix keeping fixed the total number of nitrogen bases within the DNA molecule. We take three DNA sequences, two of them are periodic and one is random and observe that in all the cases localization length increases as we increase the radius of DNA double-helix i.e., number of nucleobases within a pitch. We have also investigated the effectmore » of backbone energetic on the I-V response of the system and found that in presence of helical symmetry, depending on the interplay of conformal variation and disorder, DNA can be found in either metallic, semiconducting and insulating phases, as observed experimentally.« less

Valley-Selective Exciton Bistability in a Suspended Monolayer Semiconductor.

PubMed

Xie, Hongchao; Jiang, Shengwei; Shan, Jie; Mak, Kin Fai

2018-05-09

We demonstrate robust optical bistability, the phenomenon of two well-discriminated stable states depending upon the history of the optical input, in fully suspended monolayers of WSe 2 at low temperatures near the exciton resonance. Optical bistability has been achieved under continuous-wave optical excitation that is red-detuned from the exciton resonance at an intensity level of 10 3 W/cm 2 . The observed bistability is originated from a photothermal mechanism, which provides both optical nonlinearity and passive feedback, two essential elements for optical bistability. The low thermal conductance of suspended samples is primarily responsible for the low excitation intensities required for optical bistability. Under a finite out-of-plane magnetic field, the exciton bistability becomes helicity dependent due to the exciton valley Zeeman effect, which enables repeatable switching of the sample reflectance by light polarization. Our study has opened up exciting opportunities in controlling light with light, including its wavelength, power, and polarization, using monolayer semiconductors.

Secondary Structure Switch

ERIC Educational Resources Information Center

King, Angela G.

2006-01-01

Neurogenerative diseases like Alzheimer's disease and Parkinson's disease involve a transformation between two peptide and protein structures of alpha-helices and beta-sheets, where the peptide backbone can also participate in metal ion binding in addition to histidine residues. However, the complete absence of change in conformation of Coiled…

Helical Structure Determines Different Susceptibilities of dsDNA, dsRNA, and tsDNA to Counterion-Induced Condensation

PubMed Central

Kornyshev, Alexei A.; Leikin, Sergey

2013-01-01

Recent studies of counterion-induced condensation of nucleic acid helices into aggregates produced several puzzling observations. For instance, trivalent cobalt hexamine ions condensed double-stranded (ds) DNA oligomers but not their more highly charged dsRNA counterparts. Divalent alkaline earth metal ions condensed triple-stranded (ts) DNA oligomers but not dsDNA. Here we show that these counterintuitive experimental results can be rationalized within the electrostatic zipper model of interactions between molecules with helical charge motifs. We report statistical mechanical calculations that reveal dramatic and nontrivial interplay between the effects of helical structure and thermal fluctuations on electrostatic interaction between oligomeric nucleic acids. Combining predictions for oligomeric and much longer helices, we also interpret recent experimental studies of the role of counterion charge, structure, and chemistry. We argue that an electrostatic zipper attraction might be a major or even dominant force in nucleic acid condensation. PMID:23663846

pH-regulated metal-ligand switching in the HM loop of ATP7A: a new paradigm for metal transfer chemistry.

PubMed

Kline, Chelsey D; Gambill, Benjamin F; Mayfield, Mary; Lutsenko, Svetlana; Blackburn, Ninian J

2016-08-01

Cuproproteins such as PHM and DBM mature in late endosomal vesicles of the mammalian secretory pathway where changes in vesicle pH are employed for sorting and post-translational processing. Colocation with the P1B-type ATPase ATP7A suggests that the latter is the source of copper and supports a mechanism where selectivity in metal transfer is achieved by spatial colocation of partner proteins in their specific organelles or vesicles. In previous work we have suggested that a lumenal loop sequence located between trans-membrane helices TM1 and TM2 of the ATPase, and containing five histidines and four methionines, acts as an organelle-specific chaperone for metallation of the cuproproteins. The hypothesis posits that the pH of the vesicle regulates copper ligation and loop conformation via a mechanism which involves His to Met ligand switching induced by histidine protonation. Here we report the effect of pH on the HM loop copper coordination using X-ray absorption spectroscopy (XAS), and show via selenium substitution of the Met residues that the HM loop undergoes similar conformational switching to that found earlier for its partner PHM. We hypothesize that in the absence of specific chaperones, HM motifs provide a template for building a flexible, pH-sensitive transfer site whose structure and function can be regulated to accommodate the different active site structural elements and pH environments of its partner proteins.

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

Cooperative polymerization of α-helices induced by macromolecular architecture

NASA Astrophysics Data System (ADS)

Baumgartner, Ryan; Fu, Hailin; Song, Ziyuan; Lin, Yao; Cheng, Jianjun

2017-07-01

Catalysis observed in enzymatic processes and protein polymerizations often relies on the use of supramolecular interactions and the organization of functional elements in order to gain control over the spatial and temporal elements of fundamental cellular processes. Harnessing these cooperative interactions to catalyse reactions in synthetic systems, however, remains challenging due to the difficulty in creating structurally controlled macromolecules. Here, we report a polypeptide-based macromolecule with spatially organized α-helices that can catalyse its own formation. The system consists of a linear polymeric scaffold containing a high density of initiating groups from which polypeptides are grown, forming a brush polymer. The folding of polypeptide side chains into α-helices dramatically enhances the polymerization rate due to cooperative interactions of macrodipoles between neighbouring α-helices. The parameters that affect the rate are elucidated by a two-stage kinetic model using principles from nucleation-controlled protein polymerizations; the key difference being the irreversible nature of this polymerization.

Sequential double second-order nonlinear optical switch by an acido-triggered photochromic cyclometallated platinum(II) complex.

PubMed

Boixel, Julien; Guerchais, Véronique; Le Bozec, Hubert; Chantzis, Agisilaos; Jacquemin, Denis; Colombo, Alessia; Dragonetti, Claudia; Marinotto, Daniele; Roberto, Dominique

2015-05-07

An unprecedented DTE-based Pt(II) complex, 2(o), which stands as the first example of a sequential double nonlinear optical switch, induced first by protonation and next upon irradiation with UV light is presented.

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.

Triple Helical Recognition of Pyrimidine Inversions in Polypurine Tracts of RNA by Nucleobase-modified PNA

PubMed Central

Gupta, Pankaj; Zengeya, Thomas; Rozners, Eriks

2013-01-01

Peptide nucleic acids containing 2-pyrimidinone (P) and 3-oxo-2,3-dihydropyridazine (E) heterocycles recognized C-G and U-A inversions in a polypurine tract of double helical RNA with high affinity and sequence selectivity at pH 6.25. E-modified PNA bound strongly to bacterial A-site RNA, while no binding was observed to the human A-site RNA. PMID:21909545

Force-free electromagnetic pulses in a laboratory plasma

NASA Technical Reports Server (NTRS)

Stenzel, R. L.; Urrutia, J. M.

1990-01-01

A short, intense current pulse is drawn from an electrode immersed in a magnetized afterglow plasma. The induced magnetic field B(r,t) assumes the shape of a helical double vortex which propagates along B(0) through the uniform plasma as a whistler mode. The observations support a prediction of force-free (J x B + neE = 0) electromagnetic fields and solitary waves. Energy and helicity are approximately conserved.

Bifurcation in the MHD behaviour of a self-organizing system: the reversed field pinch (RFP)

NASA Astrophysics Data System (ADS)

Cappello, S.

2004-12-01

Within the framework of MHD modelling the RFP is shown to develop turbulent or laminar regimes switching from the former to the latter in a continuous way depending on the strength of dissipative forces (the higher they are the more laminar is the corresponding regime). In either of these cases interesting features can be observed such as the occurrence of quasi-periodic relaxation events involving reconnection processes, or the formation of stationary helical symmetric configurations. The first case corresponds to the conventional turbulent dynamo in the RFP where perturbations with multiple helical harmonic content are present. The second case corresponds to a global single helical deformation of the current channel. This simpler configuration is associated with a laminar electrostatic dynamo field and may also be found as a solution of a helical Ohmic equilibrium problem where a finite beta is necessary. The continuity of the transition between the two regimes suggests that the simple helical symmetric solution can provide a fruitful intuitive description of the RFP dynamo in general. Many of the MHD predictions are in good agreement with experimental findings and suggest possible improvements for the confinement properties of the RFP configuration.

Modeling DNA bubble formation at the atomic scale

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

Beleva, V; Rasmussen, K. O.; Garcia, A. E.

We describe the fluctuations of double stranded DNA molecules using a minimalist Go model over a wide range of temperatures. Minimalist models allow us to describe, at the atomic level, the opening and formation of bubbles in DNA double helices. This model includes all the geometrical constraints in helix melting imposed by the 3D structure of the molecule. The DNA forms melted bubbles within double helices. These bubbles form and break as a function of time. The equilibrium average number of broken base pairs shows a sharp change as a function of T. We observe a temperature profile of sequencemore » dependent bubble formation similar to those measured by Zeng et al. Long nuclei acid molecules melt partially through the formations of bubbles. It is known that CG rich sequences melt at higher temperatures than AT rich sequences. The melting temperature, however, is not solely determined by the CG content, but by the sequence through base stacking and solvent interactions. Recently, models that incorporate the sequence and nonlinear dynamics of DNA double strands have shown that DNA exhibits a very rich dynamics. Recent extensions of the Bishop-Peyrard model show that fluctuations in the DNA structure lead to opening in localized regions, and that these regions in the DNA are associated with transcription initiation sites. 1D and 2D models of DNA may contain enough information about stacking and base pairing interactions, but lack the coupling between twisting, bending and base pair opening imposed by the double helical structure of DNA that all atom models easily describe. However, the complexity of the energy function used in all atom simulations (including solvent, ions, etc) does not allow for the description of DNA folding/unfolding events that occur in the microsecond time scale.« less

Model for multishot all-thermal all-optical switching in ferromagnets

NASA Astrophysics Data System (ADS)

Gorchon, J.; Yang, Y.; Bokor, J.

2016-07-01

All-optical magnetic switching (AOS) is a recently observed rich and puzzling phenomenon that offers promising technological applications. However, a fundamental understanding of the underlying mechanisms remains elusive. Here we present a model for multishot helicity-dependent AOS in ferromagnetic materials based on a purely heat-driven mechanism in the presence of magnetic circular dichroism (MCD). We predict that AOS should be possible with as little as 0.5% of MCD, after a minimum number of laser shots heat the sample close to the Curie temperature. Finally, we qualitatively reproduce the all-optically switched domain patterns observed experimentally by numerically simulating the result of multiple laser shots on an FePtC granular ferromagnetic film.

Computerized Design and Generation of Low-noise Helical Gears with Modified Surface Topology

NASA Technical Reports Server (NTRS)

Litvin, F. L.; Chen, N. X.; Lu, J.; Handschuh, R. F.

1994-01-01

An approach for design and generation of low-noise helical gears with localized bearing contact is proposed. The approach is applied to double circular arc helical gears and modified involute helical gears. The reduction of noise and vibration is achieved by application of a predesigned parabolic function of transmission errors that is able to absorb a discontinuous linear function of transmission errors caused by misalignment. The localization of the bearing contact is achieved by the mismatch of pinion-gear tooth surfaces. Computerized simulation of meshing and contact of the designed gears demonstrated that the proposed approach will produce a pair of gears that has a parabolic transmission error function even when misalignment is present. Numerical examples for illustration of the developed approach are given.

Evaluation of helicity generation in the tropical storm Gonu

NASA Astrophysics Data System (ADS)

Farahani, Majid M.; Khansalari, Sakineh; Azadi, Majid

2017-06-01

Helicity is a valuable dynamical concept for the study of rotating flows. Consequently helicity flux, indicative of the source or sink of helicity, owns comparable importance. In this study, while reviewing the existing methods, a mathematical relation between helicity and helicity-flux is introduced, discussed and examined. The computed values of helicity and helicity fluxes in an actual case, using the classical and this proposed method are compared. The down-stream helicity flux including sources and sinks of helicity is considered for the tropical storm Gonu that occurred over the coasts of Oman and Iran on June 2-7, 2007. Results show that the buoyancy, through the upper troposphere down to a height within boundary layer, is the main source in producing helicity, and surface friction from earth surface up to a height within boundary layer, is the main dissipating element of helicity. The dominance of buoyancy forcing over the dissipative friction forcing results in generation of vortex or enhancement of it after bouncing the land. Furthermore, the increase (decrease) of helicity results in an increase (decrease) in the height of the level in which maximum helicity flux occurs. It is suggested that the maximum helicity flux occurs at the top of the turbulent boundary layer, so that the height of boundary layer could be obtained.

Conception, fabrication and characterization of a silicon based MEMS inertial switch with a threshold value of 5 g

NASA Astrophysics Data System (ADS)

Zhang, Fengtian; Wang, Chao; Yuan, Mingquan; Tang, Bin; Xiong, Zhuang

2017-12-01

Most of the MEMS inertial switches developed in recent years are intended for shock and impact sensing with a threshold value above 50 g. In order to follow the requirement of detecting linear acceleration signal at low-g level, a silicon based MEMS inertial switch with a threshold value of 5 g was designed, fabricated and characterized. The switch consisted of a large proof mass, supported by circular spiral springs. An analytical model of the structure stiffness of the proposed switch was derived and verified by finite-element simulation. The structure fabrication was based on a customized double-buried layer silicon-on-insulator wafer and encapsulated by glass wafers. The centrifugal experiment and nanoindentation experiment were performed to measure the threshold value as well as the structure stiffness. The actual threshold values were measured to be 0.1-0.3 g lower than the pre-designed value of 5 g due to the dimension loss during non-contact lithography processing. Concerning the reliability assessment, a series of environmental experiments were conducted and the switches remained operational without excessive errors. However, both the random vibration and the shock tests indicate that the metal particles generated during collision of contact parts might affect the contact reliability and long-time stability. According to the conclusion reached in this report, an attentive study on switch contact behavior should be included in future research.

Hydrodynamic studies of CNT nanofluids in helical coil heat exchanger

NASA Astrophysics Data System (ADS)

Babita; Sharma, S. K.; Mital Gupta, Shipra; Kumar, Arinjay

2017-12-01

Helical coils are extensively used in several industrial processes such as refrigeration systems, chemical reactors, recovery processes etc to accommodate a large heat transfer area within a smaller space. Nanofluids are getting great attention due to their enhanced heat transfer capability. In heat transfer equipments, pressure drop is one of the major factors of consideration for pumping power calculations. So, the present work is aimed to study hydrodynamics of CNT nanofluids in helical coils. In this study, pressure drop characteristics of CNT nanofluid flowing inside horizontal helical coils are investigated experimentally. The helical coil to tube diameter was varied from 11.71 to 27.34 keeping pitch of the helical coil constant. Double distilled water was used as basefluid. SDBS and GA surfactants were added to stablilize CNT nanofluids. The volumetric fraction of CNT nanofluid was varied from 0.003 vol% to 0.051 vol%. From the experimental data, it was analyzed that the friction factor in helical coils is greater than that of straight tubes. Concentration of CNT in nanofluids also has a significant influence on the pressure drop/friction factor of helical coils. At a constant concentration of CNT, decreasing helical coil to tube diameter from 27.24 to 11.71, fanning friction factor of helical coil; f c increases for a constant value of p/d t. This increase in the value of fanning friction factor can be attributed to the secondary flow of CNT nanofluid in helical coils.

Light-Driven Reversible Transformation between Self-Organized Simple Cubic Lattice and Helical Superstructure Enabled by a Molecular Switch Functionalized Nanocage.

PubMed

Zhou, Kang; Bisoyi, Hari Krishna; Jin, Jian-Qiu; Yuan, Cong-Long; Liu, Zhen; Shen, Dong; Lu, Yan-Qing; Zheng, Zhi-Gang; Zhang, Weian; Li, Quan

2018-04-23

Self-organized stimuli-responsive smart materials with adjustable attributes are highly desirable for a plethora of device applications. Simple cubic lattice is quite uncommon in soft condensed matter due to its lower packing factor. Achieving a stable simple cubic soft lattice and endowing such a lattice with dynamic reconstruction capability solely by a facile light irradiation are of paramount significance for both fundamental studies and engineering explorations. Herein, an elegant stable self-organized simple cubic soft lattice, i.e., blue phase II, in a chiral liquid crystal (LC) system is disclosed, which is stable down to room temperature and exhibits both reversible lattice deformation and transformation to a helical superstructure, i.e., cholesteric LC, by light stimulation. Such an amazing trait is attained by doping a judiciously designed achiral photoresponsive molecular switch functionalized polyhedral oligomeric silsesquioxane nanocage into a chiral LC host. An unprecedented reversible collapse and reconstruction of such a high symmetric simple cubic blue phase II driven by light has been achieved. Furthermore, a well-defined conglomerate micropattern composed of simple cubic soft lattice and helical superstructure, which is challenging to fabricate in organic and inorganic crystalline materials, is produced using photomasking technology. Moreover, the promising photonic application based on such a micropattern is demonstrated. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Real-Time Imaging System for Stereo Atomic Microscopy at SPring-8's BL25SU

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

Matsushita, Tomohiro; Guo, Fang Zhun; Muro, Takayuki

2007-01-19

We have developed a real-time photoelectron angular distribution (PEAD) and Auger-electron angular distribution (AEAD) imaging system at SPring-8 BL25SU, Japan. In addition, a real-time imaging system for circular dichroism (CD) studies of PEAD/AEAD has been newly developed. Two PEAD images recorded with left- and right-circularly polarized light can be regarded as a stereo image of the atomic arrangement. A two-dimensional display type mirror analyzer (DIANA) has been installed at the beamline, making it possible to record PEAD/AEAD patterns with an acceptance angle of {+-}60 deg. in real-time. The twin-helical undulators at BL25SU enable helicity switching of the circularly polarized lightmore » at 10Hz, 1Hz or 0.1Hz. In order to realize real-time measurements of the CD of the PEAD/AEAD, the CCD camera must be synchronized to the switching frequency. The VME computer that controls the ID is connected to the measurement computer with two BNC cables, and the helicity information is sent using TTL signals. For maximum flexibility, rather than using a hardware shutter synchronizing with the TTL signal we have developed software to synchronize the CCD shutter with the TTL signal. We have succeeded in synchronizing the CCD camera in both the 1Hz and 0.1Hz modes.« less

The double switch for atrioventricular discordance.

PubMed

Brawn, William J

2005-01-01

Conventional surgery for atrioventricular discordance usually associated with ventricular arterial discordance leaves the morphologic right ventricle in the systemic circulation. Long-term follow-up results with this approach reveal a high incidence of right ventricular failure. The double switch procedure was introduced to restore the morphologic left ventricle to the systemic circulation. This operation is performed in two main ways: the atrial-arterial switch and the atrial switch plus Rastelli procedure. This double switch approach has been successful at least in the medium term in abolishing morphologic right ventricular failure and its associated tricuspid valve regurgitation. In the atrial-arterial switch group, there is an incidence of morphologic left ventricular dysfunction, sometimes associated with neoaortic valve regurgitation, and the minority of cases need aortic valve replacement. The long-term function of the morphologic left ventricle and the aortic valve need careful surveillance in the future. The atrial-Rastelli group of patients has not in the medium term shown evidence of ventricular dysfunction but will require change on a regular basis of their ventricular to pulmonary artery valved conduits.

Looking for Clues to the Mystery of Life on Earth

NASA Astrophysics Data System (ADS)

Balter, Michael

1996-08-01

From the vast central hall in Chambord Castle, the largest of the great chateaux on France's River Loire, an ornate double-helical staircase rises to a roof terrace. It was an appropriate setting for a banquet of the International Society for the Study of the Origin of Life (ISSOL), which held its triennial meeting last month in nearby Orleans. Without double-helical DNA and RNA molecules, life would not exist. At the meeting, nearly 300 scientists, including three Nobel laureates, grappled with the riddle of how these molecules first appeared and how they evolved into self-reproducing cells-questions that have gained new urgency with the hint that life in some form also may have evolved on Mars (see pages 864 and 924).

A Simpler Nucleic Acid

NASA Technical Reports Server (NTRS)

Orgel, Leslie

2000-01-01

It has been supposed that for a nucleic acid analog to pair with RNA it must, like RNA, have a backbone with at least a sixatom repeat; a shorter backbone presumably would not stretch far enough to bind RNA properly. The Eschenmoser group has shown, however, that this first impression is incorrect.As they report in their new paper, Eschenmoser and co-workers ( I ) have now synthesized a substantial number of these polymers, which are called (L)-a-threofuranosyl oligonucleotides or TNAs. They are composed of bases linked to a threose sugar-phosphate backbone, with phosphodiester bonds connecting the nucleotides. The investigators discovered that pairs of complementary TNAs do indeed form stable Watson-Crick double helices and, perhaps more importantly, that TNAs form stable double helices with complementary RNAs and DNAs.

Screech tones from free and ducted supersonic jets

NASA Technical Reports Server (NTRS)

Tam, C. K. W.; Ahuja, K. K.; Jones, R. R., III

1993-01-01

The dependence of the instability wave spectrum on azimuthal mode number, the jet to ambient gas temperature ratio, and the jet Mach number is studied. It is shown that the switch of the dominant screech mode (axisymmetric to helical/flapping) as Mach number increases is due to the switch in dominance of the corresponding mode of instability waves. Super-resonance can occur when the feedback loop is powered by the most amplified instability wave. It is suggested that the large amplitude pressure fluctuations and tone in the test cells are generated by super-resonance.

Structural analysis of compression helical spring used in suspension system

NASA Astrophysics Data System (ADS)

Jain, Akshat; Misra, Sheelam; Jindal, Arun; Lakhian, Prateek

2017-07-01

The main aim of this work has to develop a helical spring for shock absorber used in suspension system which is designed to reduce shock impulse and liberate kinetic energy. In a vehicle, it increases comfort by decreasing amplitude of disturbances and it improves ride quality by absorbing and dissipating energy. When a vehicle is in motion on a road and strikes a bump, spring comes into action quickly. After compression, spring will attempt to come to its equilibrium state which is on level road. Helical springs can be made lighter with more strength by reducing number of coils and increasing the area. In this research work, a helical spring is modeled and analyzed to substitute the existing steel spring which is used in suspension. By using different materials, stress and deflection of helical spring can be varied. Comparability between existing spring and newly replaced spring is used to verify the results. For finding detailed stress distribution, finite element analysis is used to find stresses and deflection in both the helical springs. Finite element analysis is a method which is used to find proximate solutions of a physical problem defined in a finite domain. In this research work, modeling of spring is accomplished using Solid Works and analysis on Ansys.

Low-Crosstalk Composite Optical Crosspoint Switches

NASA Technical Reports Server (NTRS)

Pan, Jing-Jong; Liang, Frank

1993-01-01

Composite optical switch includes two elementary optical switches in tandem, plus optical absorbers. Like elementary optical switches, composite optical switches assembled into switch matrix. Performance enhanced by increasing number of elementary switches. Advantage of concept: crosstalk reduced to acceptably low level at moderate cost of doubling number of elementary switches rather than at greater cost of tightening manufacturing tolerances and exerting more-precise control over operating conditions.

Low-frequency switching in a transistor amplifier.

PubMed

Carroll, T L

2003-04-01

It is known from extensive work with the diode resonator that the nonlinear properties of a P-N junction can lead to period doubling, chaos, and other complicated behaviors in a driven circuit. There has been very little work on what happens when more than one P-N junction is present. In this work, the first step towards multiple P-N junction circuits is taken by doing both experiments and simulations with a single-transistor amplifier using a bipolar transistor. Period doubling and chaos are seen when the amplifier is driven with signals between 100 kHz and 1 MHz, and they coincide with a very low frequency switching between different period doubled (or chaotic) wave forms. The switching frequencies are between 5 and 10 Hz. The switching behavior was confirmed in a simplified model of the transistor amplifier.

Laser diode and pumped Cr:Yag passively Q-switched yellow-green laser at 543 nm

NASA Astrophysics Data System (ADS)

Yao, Y.; Ling, Zhao; Li, B.; Qu, D. P.; Zhou, K.; Zhang, Y. B.; Zhao, Y.; Zheng, Q.

2013-03-01

Efficient and compact yellow green pulsed laser output at 543 nm is generated by frequency doubling of a passively Q-switched end diode-pumped Nd:YVO4 laser at 1086 nm under the condition of sup-pressing the higher gain transition near 1064 nm. With 15 W of diode pump power and the frequency doubling crystal LBO, as high as 1.58 W output power at 543 nm is achieved. The optical to optical conversion efficiency from the corresponding Q-switched fundamental output to the yellow green output is 49%. The peak power of the Q-switched yellow green pulse laser is up to 30 kW with 5 ns pulse duration. The output power stability over 8 hours is better than 2.56% at the maximum output power. To the best of our knowledge, this is the highest watt-level laser at 543 nm generated by frequency doubling of a passively Q-switched end diode pumped Nd:YVO4 laser at 1086 nm.

The Cu2+-nitrilotriacetic acid complex improves loading of α-helical double histidine site for precise distance measurements by pulsed ESR

NASA Astrophysics Data System (ADS)

Ghosh, Shreya; Lawless, Matthew J.; Rule, Gordon S.; Saxena, Sunil

2018-01-01

Site-directed spin labeling using two strategically placed natural histidine residues allows for the rigid attachment of paramagnetic Cu2+. This double histidine (dHis) motif enables extremely precise, narrow distance distributions resolved by Cu2+-based pulsed ESR. Furthermore, the distance measurements are easily relatable to the protein backbone-structure. The Cu2+ ion has, till now, been introduced as a complex with the chelating agent iminodiacetic acid (IDA) to prevent unspecific binding. Recently, this method was found to have two limiting concerns that include poor selectivity towards α-helices and incomplete Cu2+-IDA complexation. Herein, we introduce an alternative method of dHis-Cu2+ loading using the nitrilotriacetic acid (NTA)-Cu2+ complex. We find that the Cu2+-NTA complex shows a four-fold increase in selectivity toward α-helical dHis sites. Furthermore, we show that 100% Cu2+-NTA complexation is achievable, enabling precise dHis loading and resulting in no free Cu2+ in solution. We analyze the optimum dHis loading conditions using both continuous wave and pulsed ESR. We implement these findings to show increased sensitivity of the Double Electron-Electron Resonance (DEER) experiment in two different protein systems. The DEER signal is increased within the immunoglobulin binding domain of protein G (called GB1). We measure distances between a dHis site on an α-helix and dHis site either on a mid-strand or a non-hydrogen bonded edge-strand β-sheet. Finally, the DEER signal is increased twofold within two α-helix dHis sites in the enzymatic dimer glutathione S-transferase exemplifying the enhanced α-helical selectivity of Cu2+-NTA.

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 occurrence of specific conformational changes due to binding of ligand or other sensory inputs in a linked upstream domain it transmits the signal to the downstream domain. Thus, the S-helix represents one of the most prevalent functional themes involved in the flow of signals between modules in diverse prokaryote-type multi-domain signaling proteins. Reviewers This article was reviewed by Frank Eisenhaber, Arcady Mushegian and Sandor Pongor. PMID:16953892

Crystal structure of a poly(rA) staggered zipper at acidic pH: evidence that adenine N1 protonation mediates parallel double helix formation

DOE PAGES

Gleghorn, Michael L.; Zhao, Jianbo; Turner, Douglas H.; ...

2016-06-10

We have solved at 1.07 Å resolution the X-ray crystal structure of a polyriboadenylic acid (poly(rA)) parallel and continuous double helix. Fifty-nine years ago, double helices of poly(rA) were first proposed to form at acidic pH. Here, we show that 7-mer oligo(rA), i.e. rA 7, hybridizes and overlaps in all registers at pH 3.5 to form stacked double helices that span the crystal. Under these conditions, rA 7 forms well-ordered crystals, whereas rA 6 forms fragile crystalline-like structures, and rA 5, rA 8 and rA 11 fail to crystallize. Our findings support studies from ~50 years ago: one showed usingmore » spectroscopic methods that duplex formation at pH 4.5 largely starts with rA 7 and begins to plateau with rA 8; another proposed a so-called ‘staggered zipper’ model in which oligo(rA) strands overlap in multiple registers to extend the helical duplex. While never shown, protonation of adenines at position N1 has been hypothesized to be critical for helix formation. Bond angles in our structure suggest that N1 is protonated on the adenines of every other rAMP–rAMP helix base pair. Lastly, our data offer new insights into poly(rA) duplex formation that may be useful in developing a pH sensor.« less

Crystal structure of a poly(rA) staggered zipper at acidic pH: evidence that adenine N1 protonation mediates parallel double helix formation

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

Gleghorn, Michael L.; Zhao, Jianbo; Turner, Douglas H.

We have solved at 1.07 Å resolution the X-ray crystal structure of a polyriboadenylic acid (poly(rA)) parallel and continuous double helix. Fifty-nine years ago, double helices of poly(rA) were first proposed to form at acidic pH. Here, we show that 7-mer oligo(rA), i.e. rA 7, hybridizes and overlaps in all registers at pH 3.5 to form stacked double helices that span the crystal. Under these conditions, rA 7 forms well-ordered crystals, whereas rA 6 forms fragile crystalline-like structures, and rA 5, rA 8 and rA 11 fail to crystallize. Our findings support studies from ~50 years ago: one showed usingmore » spectroscopic methods that duplex formation at pH 4.5 largely starts with rA 7 and begins to plateau with rA 8; another proposed a so-called ‘staggered zipper’ model in which oligo(rA) strands overlap in multiple registers to extend the helical duplex. While never shown, protonation of adenines at position N1 has been hypothesized to be critical for helix formation. Bond angles in our structure suggest that N1 is protonated on the adenines of every other rAMP–rAMP helix base pair. Lastly, our data offer new insights into poly(rA) duplex formation that may be useful in developing a pH sensor.« less

Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

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

Chojnowski, Grzegorz, E-mail: gchojnowski@genesilico.pl; Waleń, Tomasz; University of Warsaw, Banacha 2, 02-097 Warsaw

2015-03-01

A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure ismore » RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx.« less

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.

Amplitude steered array

NASA Technical Reports Server (NTRS)

Dietrich, F. J.; Koloboff, G. J.; Martel, R. J.; Johnson, C. C. (Inventor)

1974-01-01

A spin stabilized satellite has an electronically despun antenna array comprising a multiplicity of peripheral antenna elements. A high gain energy beam is established by connecting a suitable fraction or array of the elements in phase. The beam is steered or caused to scan by switching elements in sequence into one end of the array as elements at the other end of the array are switched out. The switching transients normally associated with such steering are avoided by an amplitude control system. Instead of abruptly switching from one element to the next, a fixed value of power is gradually transferred from the element at the trailing edge of the array to the element next to the leading edge.

Single-pixel computational ghost imaging with helicity-dependent metasurface hologram.

PubMed

Liu, Hong-Chao; Yang, Biao; Guo, Qinghua; Shi, Jinhui; Guan, Chunying; Zheng, Guoxing; Mühlenbernd, Holger; Li, Guixin; Zentgraf, Thomas; Zhang, Shuang

2017-09-01

Different optical imaging techniques are based on different characteristics of light. By controlling the abrupt phase discontinuities with different polarized incident light, a metasurface can host a phase-only and helicity-dependent hologram. In contrast, ghost imaging (GI) is an indirect imaging modality to retrieve the object information from the correlation of the light intensity fluctuations. We report single-pixel computational GI with a high-efficiency reflective metasurface in both simulations and experiments. Playing a fascinating role in switching the GI target with different polarized light, the metasurface hologram generates helicity-dependent reconstructed ghost images and successfully introduces an additional security lock in a proposed optical encryption scheme based on the GI. The robustness of our encryption scheme is further verified with the vulnerability test. Building the first bridge between the metasurface hologram and the GI, our work paves the way to integrate their applications in the fields of optical communications, imaging technology, and security.

Three-Dimensional Measurement of the Helicity-Dependent Forces on a Mie Particle.

PubMed

Liu, Lulu; Di Donato, Andrea; Ginis, Vincent; Kheifets, Simon; Amirzhan, Arman; Capasso, Federico

2018-06-01

Recently, it was shown that a Mie particle in an evanescent field ought to experience optical forces that depend on the helicity of the totally internally reflected beam. As yet, a direct measurement of such helicity-dependent forces has been elusive, as the widely differing force magnitudes in the three spatial dimensions place stringent demands on a measurement's sensitivity and range. In this study, we report the simultaneous measurement of all components of this polarization-dependent optical force by using a 3D force spectroscopy technique with femtonewton sensitivity. The vector force fields are compared quantitatively with our theoretical calculations as the polarization state of the incident light is varied and show excellent agreement. By plotting the 3D motion of the Mie particle in response to the switched force field, we offer visual evidence of the effect of spin momentum on the Poynting vector of an evanescent optical field.

Single-pixel computational ghost imaging with helicity-dependent metasurface hologram

PubMed Central

Liu, Hong-Chao; Yang, Biao; Guo, Qinghua; Shi, Jinhui; Guan, Chunying; Zheng, Guoxing; Mühlenbernd, Holger; Li, Guixin; Zentgraf, Thomas; Zhang, Shuang

2017-01-01

Different optical imaging techniques are based on different characteristics of light. By controlling the abrupt phase discontinuities with different polarized incident light, a metasurface can host a phase-only and helicity-dependent hologram. In contrast, ghost imaging (GI) is an indirect imaging modality to retrieve the object information from the correlation of the light intensity fluctuations. We report single-pixel computational GI with a high-efficiency reflective metasurface in both simulations and experiments. Playing a fascinating role in switching the GI target with different polarized light, the metasurface hologram generates helicity-dependent reconstructed ghost images and successfully introduces an additional security lock in a proposed optical encryption scheme based on the GI. The robustness of our encryption scheme is further verified with the vulnerability test. Building the first bridge between the metasurface hologram and the GI, our work paves the way to integrate their applications in the fields of optical communications, imaging technology, and security. PMID:28913433

Three-Dimensional Measurement of the Helicity-Dependent Forces on a Mie Particle

NASA Astrophysics Data System (ADS)

Liu, Lulu; Di Donato, Andrea; Ginis, Vincent; Kheifets, Simon; Amirzhan, Arman; Capasso, Federico

2018-06-01

Recently, it was shown that a Mie particle in an evanescent field ought to experience optical forces that depend on the helicity of the totally internally reflected beam. As yet, a direct measurement of such helicity-dependent forces has been elusive, as the widely differing force magnitudes in the three spatial dimensions place stringent demands on a measurement's sensitivity and range. In this study, we report the simultaneous measurement of all components of this polarization-dependent optical force by using a 3D force spectroscopy technique with femtonewton sensitivity. The vector force fields are compared quantitatively with our theoretical calculations as the polarization state of the incident light is varied and show excellent agreement. By plotting the 3D motion of the Mie particle in response to the switched force field, we offer visual evidence of the effect of spin momentum on the Poynting vector of an evanescent optical field.

High salt solution structure of a left-handed RNA double helix

PubMed Central

Popenda, Mariusz; Milecki, Jan; Adamiak, Ryszard W.

2004-01-01

Right-handed RNA duplexes of (CG)n sequence undergo salt-induced helicity reversal, forming left-handed RNA double helices (Z-RNA). In contrast to the thoroughly studied Z-DNA, no Z-RNA structure of natural origin is known. Here we report the NMR structure of a half-turn, left-handed RNA helix (CGCGCG)2 determined in 6 M NaClO4. This is the first nucleic acid motif determined at such high salt. Sequential assignments of non-exchangeable proton resonances of the Z-form were based on the hitherto unreported NOE connectivity path [H6(n)-H5′/H5″(n)-H8(n+1)-H1′(n+1)-H6(n+2)] found for left-handed helices. Z-RNA structure shows several conformational features significantly different from Z-DNA. Intra-strand but no inter-strand base stacking was observed for both CpG and GpC steps. Helical twist angles for CpG steps have small positive values (4–7°), whereas GpC steps have large negative values (−61°). In the full-turn model of Z-RNA (12.4 bp per turn), base pairs are much closer to the helix axis than in Z-DNA, thus both the very deep, narrow minor groove with buried cytidine 2′-OH groups, and the major groove are well defined. The 2′-OH group of cytidines plays a crucial role in the Z-RNA structure and its formation; 2′-O-methylation of cytidine, but not of guanosine residues prohibits A to Z helicity reversal. PMID:15292450

Measurements of double-helicity asymmetries in inclusive J /ψ production in longitudinally polarized p +p collisions at √{s }=510 GeV

NASA Astrophysics Data System (ADS)

Adare, A.; Aidala, C.; Ajitanand, N. N.; Akiba, Y.; Akimoto, R.; Alfred, M.; Apadula, N.; Aramaki, Y.; Asano, H.; Atomssa, E. T.; Awes, T. C.; Azmoun, B.; Babintsev, V.; Bai, M.; Bandara, N. S.; Bannier, B.; Barish, K. N.; Bathe, S.; Bazilevsky, A.; Beaumier, M.; Beckman, S.; Belmont, R.; Berdnikov, A.; Berdnikov, Y.; Black, D.; Blau, D. S.; Bok, J. S.; Boyle, K.; Brooks, M. L.; Bryslawskyj, J.; Buesching, H.; Bumazhnov, V.; Campbell, S.; Chen, C.-H.; Chi, C. Y.; Chiu, M.; Choi, I. J.; Choi, J. B.; Chujo, T.; Citron, Z.; Csanád, M.; Csörgő, T.; Danley, T. W.; Datta, A.; Daugherity, M. S.; David, G.; Deblasio, K.; Dehmelt, K.; Denisov, A.; Deshpande, A.; Desmond, E. J.; Ding, L.; Dion, A.; Diss, P. B.; Do, J. H.; Drees, A.; Drees, K. A.; Durham, J. M.; Durum, A.; Enokizono, A.; En'yo, H.; Esumi, S.; Fadem, B.; Feege, N.; Fields, D. E.; Finger, M.; Finger, M.; Fokin, S. L.; Frantz, J. E.; Franz, A.; Frawley, A. D.; Gal, C.; Gallus, P.; Garg, P.; Ge, H.; Giordano, F.; Glenn, A.; Goto, Y.; Grau, N.; Greene, S. V.; Grosse Perdekamp, M.; Gu, Y.; Gunji, T.; Guragain, H.; Hachiya, T.; Haggerty, J. S.; Hahn, K. I.; Hamagaki, H.; Hamilton, H. F.; Han, S. Y.; Hanks, J.; Hasegawa, S.; Haseler, T. O. S.; Hashimoto, K.; He, X.; Hemmick, T. K.; Hill, J. C.; Hollis, R. S.; Homma, K.; Hong, B.; Hoshino, T.; Hotvedt, N.; Huang, J.; Huang, S.; Ikeda, Y.; Imai, K.; Imazu, Y.; Inaba, M.; Iordanova, A.; Isenhower, D.; Ivanishchev, D.; Jacak, B. V.; Jeon, S. J.; Jezghani, M.; Jia, J.; Jiang, X.; Johnson, B. M.; Joo, E.; Joo, K. S.; Jouan, D.; Jumper, D. S.; Kanda, S.; Kang, J. H.; Kang, J. S.; Kawall, D.; Kazantsev, A. V.; Key, J. A.; Khachatryan, V.; Khanzadeev, A.; Kihara, K.; Kim, C.; Kim, D. H.; Kim, D. J.; Kim, E.-J.; Kim, G. W.; Kim, H.-J.; Kim, M.; Kim, Y. K.; Kimelman, B.; Kistenev, E.; Kitamura, R.; Klatsky, J.; Kleinjan, D.; Kline, P.; Koblesky, T.; Kofarago, M.; Komkov, B.; Koster, J.; Kotov, D.; Kurita, K.; Kurosawa, M.; Kwon, Y.; Lacey, R.; Lajoie, J. G.; Lebedev, A.; Lee, K. B.; Lee, S.; Lee, S. H.; Leitch, M. J.; Leitgab, M.; Li, X.; Lim, S. H.; Liu, M. X.; Lynch, D.; Makdisi, Y. I.; Makek, M.; Manion, A.; Manko, V. I.; Mannel, E.; McCumber, M.; McGaughey, P. L.; McGlinchey, D.; McKinney, C.; Meles, A.; Mendoza, M.; Meredith, B.; Miake, Y.; Mignerey, A. C.; Miller, A. J.; Milov, A.; Mishra, D. K.; Mitchell, J. T.; Miyasaka, S.; Mizuno, S.; Mohanty, A. K.; Montuenga, P.; Moon, T.; Morrison, D. P.; Moukhanova, T. V.; Murakami, T.; Murata, J.; Mwai, A.; Nagamiya, S.; Nagashima, K.; Nagle, J. L.; Nagy, M. I.; Nakagawa, I.; Nakagomi, H.; Nakano, K.; Nattrass, C.; Netrakanti, P. K.; Nihashi, M.; Niida, T.; Nishimura, S.; Nouicer, R.; Novák, T.; Novitzky, N.; Nyanin, A. S.; O'Brien, E.; Ogilvie, C. A.; Orjuela Koop, J. D.; Osborn, J. D.; Oskarsson, A.; Ozawa, K.; Pak, R.; Pantuev, V.; Papavassiliou, V.; Park, J. S.; Park, S.; Pate, S. F.; Patel, L.; Patel, M.; Peng, J.-C.; Perepelitsa, D. V.; Perera, G. D. N.; Peressounko, D. Yu.; Perry, J.; Petti, R.; Pinkenburg, C.; Pinson, R.; Pisani, R. P.; Purschke, M. L.; Rak, J.; Ramson, B. J.; Ravinovich, I.; Read, K. F.; Reynolds, D.; Riabov, V.; Riabov, Y.; Rinn, T.; Riveli, N.; Roach, D.; Rolnick, S. D.; Rosati, M.; Rowan, Z.; Rubin, J. G.; Sahlmueller, B.; Saito, N.; Sakaguchi, T.; Sako, H.; Samsonov, V.; Sarsour, M.; Sato, S.; Sawada, S.; Schaefer, B.; Schmoll, B. K.; Sedgwick, K.; Seele, J.; Seidl, R.; Sen, A.; Seto, R.; Sett, P.; Sexton, A.; Sharma, D.; Shein, I.; Shibata, T.-A.; Shigaki, K.; Shimomura, M.; Shukla, P.; Sickles, A.; Silva, C. L.; Silvermyr, D.; Singh, B. K.; Singh, C. P.; Singh, V.; Slunečka, M.; Snowball, M.; Soltz, R. A.; Sondheim, W. E.; Sorensen, S. P.; Sourikova, I. V.; Stankus, P. W.; Stepanov, M.; Stoll, S. P.; Sugitate, T.; Sukhanov, A.; Sumita, T.; Sun, J.; Sziklai, J.; Takahara, A.; Taketani, A.; Tanida, K.; Tannenbaum, M. J.; Tarafdar, S.; Taranenko, A.; Tieulent, R.; Timilsina, A.; Todoroki, T.; Tomášek, M.; Torii, H.; Towell, C. L.; Towell, M.; Towell, R.; Towell, R. S.; Tserruya, I.; van Hecke, H. W.; Vargyas, M.; Velkovska, J.; Virius, M.; Vrba, V.; Vznuzdaev, E.; Wang, X. R.; Watanabe, D.; Watanabe, Y.; Watanabe, Y. S.; Wei, F.; Whitaker, S.; White, A. S.; Wolin, S.; Woody, C. L.; Wysocki, M.; Xia, B.; Xue, L.; Yalcin, S.; Yamaguchi, Y. L.; Yanovich, A.; Yoo, J. H.; Yoon, I.; Younus, I.; Yu, H.; Yushmanov, I. E.; Zajc, W. A.; Zelenski, A.; Zhou, S.; Zou, L.; Phenix Collaboration

2016-12-01

We report the double-helicity asymmetry, ALL J /ψ, in inclusive J /ψ production at forward rapidity as a function of transverse momentum pT and rapidity |y |. The data analyzed were taken during √{s }=510 GeV longitudinally polarized p +p collisions at the Relativistic Heavy Ion Collider in the 2013 run using the PHENIX detector. At this collision energy, J /ψ particles are predominantly produced through gluon-gluon scatterings, thus ALL J /ψ is sensitive to the gluon polarization inside the proton. We measured ALL J /ψ by detecting the decay daughter muon pairs μ+μ- within the PHENIX muon spectrometers in the rapidity range 1.2 <|y |<2.2 . In this kinematic range, we measured the ALL J /ψ to be 0.012 ±0.010 (stat) ±0.003 (syst). The ALL J /ψ can be expressed to be proportional to the product of the gluon polarization distributions at two distinct ranges of Bjorken x : one at moderate range x ≈5 ×10-2 where recent data of jet and π0 double helicity spin asymmetries have shown evidence for significant gluon polarization, and the other one covering the poorly known small-x region x ≈2 ×10-3. Thus our new results could be used to further constrain the gluon polarization for x <5 ×10-2.

Dual-cone double-helical downhole logging device

DOEpatents

Yu, Jiunn S.

1984-01-01

A broadband downhole logging device includes a double-helix coil wrapped over a dielectric support and surrounded by a dielectric shield. The device may also include a second coil longitudinally aligned with a first coil and enclosed within the same shield for measuring magnetic permeability of downhole formations and six additional coils for accurately determining downhole parameters.

Organic non-volatile resistive photo-switches for flexible image detector arrays.

PubMed

Nau, Sebastian; Wolf, Christoph; Sax, Stefan; List-Kratochvil, Emil J W

2015-02-01

A unique implementation of an organic image detector using resistive photo-switchable pixels is presented. This resistive photo-switch comprises the vertical integration of an organic photodiode and an organic resistive switching memory element. The photodiodes act as a photosensitive element while the resistive switching elements simultaneously store the detected light information. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Generating a Double-Scroll Attractor by Connecting a Pair of Mutual Mirror-Image Attractors via Planar Switching Control

NASA Astrophysics Data System (ADS)

Sun, Changchun; Chen, Zhongtang; Xu, Qicheng

2017-12-01

An original three-dimensional (3D) smooth continuous chaotic system and its mirror-image system with eight common parameters are constructed and a pair of symmetric chaotic attractors can be generated simultaneously. Basic dynamical behaviors of two 3D chaotic systems are investigated respectively. A double-scroll chaotic attractor by connecting the pair of mutual mirror-image attractors is generated via a novel planar switching control approach. Chaos can also be controlled to a fixed point, a periodic orbit and a divergent orbit respectively by switching between two chaotic systems. Finally, an equivalent 3D chaotic system by combining two 3D chaotic systems with a switching law is designed by utilizing a sign function. Two circuit diagrams for realizing the double-scroll attractor are depicted by employing an improved module-based design approach.

Rugged switch responds to minute pressure differentials

NASA Technical Reports Server (NTRS)

Friend, L. C.; Shaub, K. D.

1967-01-01

Pressure responsive switching device exhibits high sensitivity but is extremely rugged and resistant to large amplitude shock and velocity loading. This snap-action, single pole-double throw switch operates over a wide temperature range.

Q-switched pulse laser generation from double-cladding Nd:YAG ceramics waveguides.

PubMed

Tan, Yang; Luan, Qingfang; Liu, Fengqin; Chen, Feng; Vázquez de Aldana, Javier Rodríguez

2013-08-12

This work reports on the Q-switched pulsed laser generation from double-cladding Nd:YAG ceramic waveguides. Double-cladding waveguides with different combination of diameters were inscribed into a sample of Nd:YAG ceramic. With an additional semiconductor saturable absorber, stable pulsed laser emission at the wavelength of 1064 nm was achieved with pulses of 21 ns temporal duration and ~14 μJ pulse energy at a repetition rate of 3.65 MHz.

PINCHED PLASMA REACTOR

DOEpatents

Phillips, J.A.; Suydam, R.; Tuck, J.L.

1961-07-01

BS>A plasma confining and heating reactor is described which has the form of a torus with a B/sub 2/ producing winding on the outside of the torus and a helical winding of insulated overlapping tunns on the inside of the torus. The inner helical winding performs the double function of shielding the plasma from the vitreous container and generating a second B/sub z/ field in the opposite direction to the first B/sub z/ field after the pinch is established.

First measurement of the double spin asymmetry in (-->)e(-->)p-->e(prime)pi(+)n in the resonance region.

PubMed

De Vita, R; Anghinolfi, M; Burkert, V D; Dodge, G E; Minehart, R; Taiuti, M; Weller, H; Adams, G; Amaryan, M J; Anciant, E; Armstrong, D S; Asavapibhop, B; Asryan, G; Audit, G; Auger, T; Avakian, H; Bagdasaryan, H; Ball, J P; Barrow, S; Battaglieri, M; Beard, K; Bektasoglu, M; Bianchi, N; Biselli, A S; Boiarinov, S; Bonner, B E; Bosted, P; Bouchigny, S; Branford, D; Brooks, W K; Bueltmann, S; Calarco, J R; Capitani, G P; Carman, D S; Carnahan, B; Cazes, A; Ciciani, L; Cole, P L; Coleman, A; Connelly, J; Cords, D; Corvisiero, P; Crabb, D; Crannell, H; Cummings, J P; De Sanctis, E; Degtyarenko, P V; Demirchyan, R; Denizli, H; Dennis, L; Dharmawardane, K V; Dhuga, K S; Djalali, C; Doughty, D; Dragovitsch, P; Dugger, M; Dytman, S; Eckhause, M; Egiyan, H; Egiyan, K S; Elouadrhiri, L; Empl, A; Farhi, L; Fatemi, R; Feuerbach, R J; Ficenec, J; Forest, T A; Frolov, V; Funsten, H; Gaff, S J; Gai, M; Garçon, M; Gavalian, G; Gilad, S; Gilfoyle, G P; Giovanetti, K L; Girard, P; Golovatch, E; Griffioen, K; Guidal, M; Guillo, M; Gyurjyan, V; Hadjidakis, C; Hancock, D; Hardie, J; Heddle, D; Heimberg, P; Hersman, F W; Hicks, K; Hicks, R S; Holtrop, M; Hu, J; Hyde-Wright, C E; Ishkanov, B S; Ito, M M; Jenkins, D; Joo, K; Kelley, J H; Kellie, J D; Khandaker, M; Kim, K Y; Kim, K; Kim, W; Klein, A; Klein, F J; Klusman, M; Kossov, M; Kramer, L H; Kuang, Y; Kuhn, S E; Lachniet, J; Laget, J M; Lawrence, D; Li, Ji; Livingston, K; Longhi, A; Loukachine, K; Lucas, M; Major, W; Manak, J J; Marchand, C; McAleer, S; McCarthy, J; McNabb, J W C; Mecking, B A; Mestayer, M D; Meyer, C A; Mikhailov, K; Mirazita, M; Miskimen, R; Mokeev, V; Muccifora, V; Mueller, J; Mutchler, G S; Napolitano, J; Nelson, S O; Niculescu, G; Niculescu, I; Niczyporuk, B B; Niyazov, R A; Opper, A K; O'Rielly, G V; Osipenko, M; Park, K; Pasyuk, E; Peterson, G; Philips, S A; Pivnyuk, N; Pocanic, D; Pogorelko, O; Polli, E; Pozdniakov, S; Preedom, B M; Price, J W; Prok, Y; Protopopescu, D; Qin, L M; Raue, B A; Reolon, A R; Riccardi, G; Ricco, G; Ripani, M; Ritchie, B G; Rock, S; Ronchetti, F; Rossi, P; Rowntree, D; Rubin, P D; Sabatié, F; Sabourov, K; Salgado, C; Sapunenko, V; Sargsyan, M; Schumacher, R A; Serov, V S; Shafi, A; Sharabian, Y G; Shaw, J; Skabelin, A V; Smith, E S; Smith, T; Smith, L C; Sober, D I; Sorrell, L; Spraker, M; Stavinsky, A; Stepanyan, S; Stoler, P; Strakovsky, I I; Taylor, S; Tedeschi, D J; Thompson, R; Todor, L; Ungaro, M; Vineyard, M F; Vlassov, A V; Wang, K; Weinstein, L B; Weisberg, A; Weygand, D P; Whisnant, C S; Wolin, E; Yegneswaran, A; Yun, J; Zhang, B; Zhao, J; Zhou, Z

2002-02-25

The double spin asymmetry in the (-->)e(-->)p --> e(prime)pi(+)n reaction has been measured for the first time in the resonance region for four-momentum transfer Q2 = 0.35-1.5 GeV(2). Data were taken at Jefferson Lab with the CLAS detector using a 2.6 GeV polarized electron beam incident on a polarized solid NH3 target. Comparison with predictions of phenomenological models shows strong sensitivity to resonance contributions. Helicity-1/2 transitions are found to be dominant in the second and third resonance regions. The measured asymmetry is consistent with a faster rise with Q(2) of the helicity asymmetry A1 for the F(15)(1680) resonance than expected from the analysis of the unpolarized data.

Dimerization of the SP1 Region of HIV-1 Gag Induces a Helical Conformation and Association into Helical Bundles: Implications for Particle Assembly.

PubMed

Datta, Siddhartha A K; Clark, Patrick K; Fan, Lixin; Ma, Buyong; Harvin, Demetria P; Sowder, Raymond C; Nussinov, Ruth; Wang, Yun-Xing; Rein, Alan

2016-02-15

HIV-1 immature particle (virus-like particle [VLP]) assembly is mediated largely by interactions between the capsid (CA) domains of Gag molecules but is facilitated by binding of the nucleocapsid (NC) domain to nucleic acid. We previously investigated the role of SP1, a "spacer" between CA and NC, in VLP assembly. We found that small changes in SP1 drastically disrupt assembly and that a peptide representing the sequence around the CA-SP1 junction is helical at high but not low concentrations. We suggested that by virtue of such a concentration-dependent change, this region could act as a molecular switch to activate HIV-1 Gag for VLP assembly. A leucine zipper domain can replace NC in Gag and still lead to the efficient assembly of VLPs. We find that SP1 mutants also disrupt assembly by these Gag-Zip proteins and have now studied a small fragment of this Gag-Zip protein, i.e., the CA-SP1 junction region fused to a leucine zipper. Dimerization of the zipper places SP1 at a high local concentration, even at low total concentrations. In this context, the CA-SP1 junction region spontaneously adopts a helical conformation, and the proteins associate into tetramers. Tetramerization requires residues from both CA and SP1. The data suggest that once this region becomes helical, its propensity to self-associate could contribute to Gag-Gag interactions and thus to particle assembly. There is complete congruence between CA/SP1 sequences that promote tetramerization when fused to zippers and those that permit the proper assembly of full-length Gag; thus, equivalent interactions apparently participate in VLP assembly and in SP1-Zip tetramerization. Assembly of HIV-1 Gag into virus-like particles (VLPs) appears to require an interaction with nucleic acid, but replacement of its principal nucleic acid-binding domain with a dimerizing leucine zipper domain leads to the assembly of RNA-free VLPs. It has not been clear how dimerization triggers assembly. Results here show that the SP1 region spontaneously switches to a helical state when fused to a leucine zipper and that these helical molecules further associate into tetramers, mediated by interactions between hydrophobic faces of the helices. Thus, the correct juxtaposition of the SP1 region makes it "association competent." Residues from both capsid and SP1 contribute to tetramerization, while mutations disrupting proper assembly in Gag also prevent tetramerization. Thus, this region is part of an associating interface within Gag, and its intermolecular interactions evidently help stabilize the immature Gag lattice. These interactions are disrupted by proteolysis of the CA-SP1 junction during virus maturation. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Dimerization of the SP1 Region of HIV-1 Gag Induces a Helical Conformation and Association into Helical Bundles: Implications for Particle Assembly

PubMed Central

Clark, Patrick K.; Fan, Lixin; Ma, Buyong; Harvin, Demetria P.; Sowder, Raymond C.; Nussinov, Ruth; Wang, Yun-Xing

2015-01-01

ABSTRACT HIV-1 immature particle (virus-like particle [VLP]) assembly is mediated largely by interactions between the capsid (CA) domains of Gag molecules but is facilitated by binding of the nucleocapsid (NC) domain to nucleic acid. We previously investigated the role of SP1, a “spacer” between CA and NC, in VLP assembly. We found that small changes in SP1 drastically disrupt assembly and that a peptide representing the sequence around the CA-SP1 junction is helical at high but not low concentrations. We suggested that by virtue of such a concentration-dependent change, this region could act as a molecular switch to activate HIV-1 Gag for VLP assembly. A leucine zipper domain can replace NC in Gag and still lead to the efficient assembly of VLPs. We find that SP1 mutants also disrupt assembly by these Gag-Zip proteins and have now studied a small fragment of this Gag-Zip protein, i.e., the CA-SP1 junction region fused to a leucine zipper. Dimerization of the zipper places SP1 at a high local concentration, even at low total concentrations. In this context, the CA-SP1 junction region spontaneously adopts a helical conformation, and the proteins associate into tetramers. Tetramerization requires residues from both CA and SP1. The data suggest that once this region becomes helical, its propensity to self-associate could contribute to Gag-Gag interactions and thus to particle assembly. There is complete congruence between CA/SP1 sequences that promote tetramerization when fused to zippers and those that permit the proper assembly of full-length Gag; thus, equivalent interactions apparently participate in VLP assembly and in SP1-Zip tetramerization. IMPORTANCE Assembly of HIV-1 Gag into virus-like particles (VLPs) appears to require an interaction with nucleic acid, but replacement of its principal nucleic acid-binding domain with a dimerizing leucine zipper domain leads to the assembly of RNA-free VLPs. It has not been clear how dimerization triggers assembly. Results here show that the SP1 region spontaneously switches to a helical state when fused to a leucine zipper and that these helical molecules further associate into tetramers, mediated by interactions between hydrophobic faces of the helices. Thus, the correct juxtaposition of the SP1 region makes it “association competent.” Residues from both capsid and SP1 contribute to tetramerization, while mutations disrupting proper assembly in Gag also prevent tetramerization. Thus, this region is part of an associating interface within Gag, and its intermolecular interactions evidently help stabilize the immature Gag lattice. These interactions are disrupted by proteolysis of the CA-SP1 junction during virus maturation. PMID:26637452

Thermal or nonthermal? That is the question for ultrafast spin switching in GdFeCo.

PubMed

Zhang, G P; George, Thomas F

2013-09-11

GdFeCo is among the most interesting magnets for producing laser-induced femtosecond magnetism, where light can switch its spin moment from one direction to another. This paper aims to set a criterion for the thermal/nonthermal mechanism: we propose to use the Fermi-Dirac distribution function as a reliable criterion. A precise value for the thermalization time is needed, and through a two-level model, we show that since there is no direct connection between the laser helicity and the definition of thermal/nonthermal processes, the helicity is a poor criterion for differentiating a thermal from a nonthermal process. In addition, we propose a four-site model system (Gd2Fe2) for investigating the transient ferromagnetic ordering between Gd and Fe ions. We find that states of two different kinds can allow such an ordering. One state is a pure ferromagnetic state with ferromagnetic ordering among all the ions, and the other is the short-ranged ferromagnetic ordering of a pair of Gd and Fe ions.

The structural coupling between ATPase activation and recovery stroke in the myosin II motor

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

Koppole, Sampath; Smith, Jeremy C; Fischer, S.

2007-07-01

Before the myosin motor head can perform the next power stroke, it undergoes a large conformational transition in which the converter domain, bearing the lever arm, rotates {approx} 65{sup o}. Simultaneous with this 'recovery stroke', myosin activates its ATPase function by closing the Switch-2 loop over the bound ATP. This coupling between the motions of the converter domain and of the 40 {angstrom}-distant Switch-2 loop is essential to avoid unproductive ATP hydrolysis. The coupling mechanism is determined here by finding a series of optimized intermediates between crystallographic end structures of the recovery stroke (Dictyostelium discoideum), yielding movies of the transitionmore » at atomic detail. The successive formation of two hydrogen bonds by the Switch-2 loop is correlated with the successive see-saw motions of the relay and SH1 helices that hold the converter domain. SH1 helix and Switch-2 loop communicate via a highly conserved loop that wedges against the SH1-helix upon Switch-2 closing.« less

The structural coupling between ATPase activation and recovery stroke in the myosin II motor.

PubMed

Koppole, Sampath; Smith, Jeremy C; Fischer, Stefan

2007-07-01

Before the myosin motor head can perform the next power stroke, it undergoes a large conformational transition in which the converter domain, bearing the lever arm, rotates approximately 65 degrees . Simultaneous with this "recovery stroke," myosin activates its ATPase function by closing the Switch-2 loop over the bound ATP. This coupling between the motions of the converter domain and of the 40 A-distant Switch-2 loop is essential to avoid unproductive ATP hydrolysis. The coupling mechanism is determined here by finding a series of optimized intermediates between crystallographic end structures of the recovery stroke (Dictyostelium discoideum), yielding movies of the transition at atomic detail. The successive formation of two hydrogen bonds by the Switch-2 loop is correlated with the successive see-saw motions of the relay and SH1 helices that hold the converter domain. SH1 helix and Switch-2 loop communicate via a highly conserved loop that wedges against the SH1-helix upon Switch-2 closing.

Planar optics with patterned chiral liquid crystals

NASA Astrophysics Data System (ADS)

Kobashi, Junji; Yoshida, Hiroyuki; Ozaki, Masanori

2016-06-01

Reflective metasurfaces based on metallic and dielectric nanoscatterers have attracted interest owing to their ability to control the phase of light. However, because such nanoscatterers require subwavelength features, the fabrication of elements that operate in the visible range is challenging. Here, we show that chiral liquid crystals with a self-organized helical structure enable metasurface-like, non-specular reflection in the visible region. The phase of light that is Bragg-reflected off the helical structure can be controlled over 0-2π depending on the spatial phase of the helical structure; thus planar elements with arbitrary reflected wavefronts can be created via orientation control. The circular polarization selectivity and external field tunability of Bragg reflection open a wide variety of potential applications for this family of functional devices, from optical isolators to wearable displays.

Expansion of epicyclic gear dynamic analysis program

NASA Technical Reports Server (NTRS)

Boyd, Linda Smith; Pike, James A.

1987-01-01

The multiple mesh/single stage dynamics program is a gear tooth analysis program which determines detailed geometry, dynamic loads, stresses, and surface damage factors. The program can analyze a variety of both epicyclic and single mesh systems with spur or helical gear teeth including internal, external, and buttress tooth forms. The modifications refine the options for the flexible carrier and flexible ring gear rim and adds three options: a floating Sun gear option; a natural frequency option; and a finite element compliance formulation for helical gear teeth. The option for a floating Sun incorporates two additional degrees of freedom at the Sun center. The natural frequency option evaluates the frequencies of planetary, star, or differential systems as well as the effect of additional springs at the Sun center and those due to a flexible carrier and/or ring gear rim. The helical tooth pair finite element calculated compliance is obtained from an automated element breakup of the helical teeth and then is used with the basic gear dynamic solution and stress postprocessing routines. The flexible carrier or ring gear rim option for planetary and star spur gear systems allows the output torque per carrier and ring gear rim segment to vary based on the dynamic response of the entire system, while the total output torque remains constant.

Ligand reprogramming in dinuclear helicate complexes: a consequence of allosteric or electrostatic effects?

PubMed

Jeffery, John C; Rice, Craig R; Harding, Lindsay P; Baylies, Christian J; Riis-Johannessen, Thomas

2007-01-01

The ditopic ligand 6,6'-bis(4-methylthiazol-2-yl)-3,3'-([18]crown-6)-2,2'-bipyridine (L(1)) contains both a potentially tetradentate pyridyl-thiazole (py-tz) N-donor chain and an additional "external" crown ether binding site which spans the central 2,2'-bipyridine unit. In polar solvents (MeCN, MeNO(2)) this ligand forms complexes with Zn(II), Cd(II), Hg(II) and Cu(I) ions via coordination of the N donors to the metal ion. Reaction with both Hg(II) and Cu(I) ions results in the self-assembly of dinuclear double-stranded helicate complexes. The ligands are partitioned by rotation about the central py--py bond, such that each can coordinate to both metals as a bis-bidentate donor ligand. With Zn(II) ions a single-stranded mononuclear species is formed in which one ligand coordinates the metal ion in a planar tetradentate fashion. Reaction with Cd(II) ions gives rise to an equilibrium between both the dinuclear double-stranded helicate and the mononuclear species. These complexes can further coordinate s-block metal cations via the remote crown ether O-donor domains; a consequence of which are some remarkable changes in the binding modes of the N-donor domains. Reaction of the Hg(II)- or Cd(II)-containing helicate with either Ba(2+) or Sr(2+) ions effectively reprogrammes the ligand to form only the single-stranded heterobinuclear complexes [MM'(L(1))](4+) (M=Hg(II), Cd(II); M'=Ba(2+), Sr(2+)), where the transition and s-block cations reside in the N- and O-donor sites, respectively. In contrast, the same ions have only a minor structural impact on the Zn(II) species, which already exists as a single-stranded mononuclear complex. Similar reactions with the Cd(II) system result in a shift in equilibrium towards the single-stranded species, the extent of which depends on the size and charge of the s-block cation in question. Reaction of the dicopper(I) double-stranded helicate with Ba(2+) shows that the dinuclear structure still remains intact but the pitch length is significantly increased.

Refoldable Foldamers: Global Conformational Switching by Deletion or Insertion of a Single Hydrogen Bond

PubMed Central

Le Bailly, Bryden A. F.; Byrne, Liam

2016-01-01

Abstract Small changes in the structure of a foldamer may lead to gross changes in conformational preference. We show that the simple insertion or deletion of a single hydrogen bond by changes in pH or by photochemical deprotection is sufficient to refold a helical oligomer, interconverting M and P screw‐sense preference. As a consequence of the switch, information may be transmitted to a remote catalytic site, selectively directing the formation of either of two enantiomeric products by a reaction involving 1,22‐remote intermolecular asymmetric induction. PMID:26762559

Control of reversible magnetization switching by pulsed circular magnetic field in glass-coated amorphous microwires

NASA Astrophysics Data System (ADS)

Chizhik, Alexander; Zhukov, Arkady; Gonzalez, Julian; Stupakiewicz, Andrzej

2018-02-01

Magnetization reversal in magnetic microwires was studied in the presence of external mechanical stress and helical magnetic fields using the magneto-optical Kerr effect. It was found that a combination of tuned magnetic anisotropy and a direct current or pulsed circular magnetic field activated different types of magnetization reversal scenarios. The application of the pulsed magnetic field of 10 ns time duration induced a transient controlling action to switch the magnetic states without activating a domain wall motion. This created a promising method for tuning the giant magneto-impedance effect.

Helicity-dependent all-optical switching in hybrid metal-ferromagnet structures for ultrafast magnetic data storage

NASA Astrophysics Data System (ADS)

Cheng, Feng

The emerging Big Data era demands the rapidly increasing need for speed and capacity of storing and processing information. Standalone magnetic recording devices, such as hard disk drives (HDDs), have always been playing a central role in modern data storage and continuously advancing. Recognizing the growing capacity gap between the demand and production, industry has pushed the bit areal density in HDDs to 900 Giga-bit/square-inch, a remarkable 450-million-fold increase since the invention of the first hard disk drive in 1956. However, the further development of HDD capacity is facing a pressing challenge, the so-called superparamagnetic effect, that leads to the loss of information when a single bit becomes too small to preserve the magnetization. This requires new magnetic recording technologies that can write more stable magnetic bits into hard magnetic materials. Recent research has shown that it is possible to use ultrafast laser pulses to switch the magnetization in certain types of magnetic thin films. Surprisingly, such a process does not require an externally applied magnetic field that always exists in conventional HDDs. Furthermore, the optically induced magnetization switching is extremely fast, up to sub-picosecond (10 -12 s) level, while with traditional recording method the deterministic switching does not take place shorter than 20 ps. It's worth noting that the direction of magnetization is related to the helicity of the incident laser pulses. Namely, the right-handed polarized laser pulses will generate magnetization pointing in one direction while left-handed polarized laser pulses generate magnetization pointing in the other direction. This so-called helicity-dependent all-optical switching (HD-AOS) phenomenon can be potentially used in the next-generation of magnetic storage systems. In this thesis, I explore the HD-AOS phenomenon in hybrid metal-ferromagnet structures, which consist of gold and Co/Pt multilayers. The experiment results show that such CoPtAu hybrid structures have stable HD-AOS phenomenon over a wild range of repetition rates and peak powers. A macroscopic three-temperature model is developed to explain the experiment results. In order to reduce the magnetic bit size and power consumption to transform future magnetic data storage techniques, I further propose plasmonic-enhanced all-optical switching (PE-AOS) by utilizing the unique properties of the tight field confinement and strong local field enhancement that arise from the excitation of surface plasmons supported by judiciously designed metallic nanostructures. The preliminary results on PE-AOS are presented. Finally, I provide a discussion on the future work to explore the underline mechanism of the HD-AOS phenomenon in hybrid metal-ferromagnetic thin films. Different materials and plasmonic nanostructures are also proposed as further work.

Double-Edged Innovations: Preventing the Misuse of Emerging Biological/Chemical Technologies

DTIC Science & Technology

2010-07-01

1953 paper describing the double-helical structure of the DNA molecule and suggesting a mechanism for its replication. In 1973, Stanley Cohen of...Virology in early 2001. The security implications of the paper , however, triggered a storm of...unexpected findings of the mousepox experiment could have been predicted because a paper describing the role of interleukin-4 in poxvirus virulence

Single-Pole Double-Throw MMIC Switches for a Microwave Radiometer

NASA Technical Reports Server (NTRS)

Montes, Oliver; Dawson, Douglas E.; Kangaslahti, Pekka P.

2012-01-01

In order to reduce the effect of gain and noise instabilities in the RF chain of a microwave radiometer, a Dicke radiometer topology is often used, as in the case of the proposed surface water and ocean topography (SWOT) radiometer instrument. For this topology, a single-pole double-throw (SPDT) microwave switch is needed, which must have low insertion loss at the radiometer channel frequencies to minimize the overall receiver noise figure. Total power radiometers are limited in accuracy due to the continuous variation in gain of the receiver. High-frequency SPDT switches were developed in the form of monolithic microwave integrated circuits (MMICs) using 75 micron indium phosphide (InP) PIN-diode technology. These switches can be easily integrated into Dicke switched radiometers that utilize microstrip technology.

Design of photonic phased array switches using nano electromechanical systems on silicon-on-insulator integration platform

NASA Astrophysics Data System (ADS)

Hussein, Ali Abdulsattar

This thesis presents an introduction to the design and simulation of a novel class of integrated photonic phased array switch elements. The main objective is to use nano-electromechanical (NEMS) based phase shifters of cascaded under-etched slot nanowires that are compact in size and require a small amount of power to operate them. The structure of the switch elements is organized such that it brings the phase shifting elements to the exterior sides of the photonic circuits. The transition slot couplers, used to interconnect the phase shifters, are designed to enable biasing one of the silicon beams of each phase shifter from an electrode located at the side of the phase shifter. The other silicon beam of each phase shifter is biased through the rest of the silicon structure of the switch element, which is taken as a ground. Phased array switch elements ranging from 2x2 up to 8x8 multiple-inputs/multiple-outputs (MIMO) are conveniently designed within reasonable footprints native to the current fabrication technologies. Chapter one presents the general layout of the various designs of the switch elements and demonstrates their novel features. This demonstration will show how waveguide disturbances in the interconnecting network from conventional switch elements can be avoided by adopting an innovative design. Some possible applications for the designed switch elements of different sizes and topologies are indicated throughout the chapter. Chapter two presents the design of the multimode interference (MMI) couplers used in the switch elements as splitters, combiners and waveguide crossovers. Simulation data and design methodologies for the multimode couplers of interest are detailed in this chapter. Chapter three presents the design and analysis of the NEMS-operated phase shifters. Both simulations and numerical analysis are utilized in the design of a 0°-180° capable NEMS-operated phase shifter. Additionally, the response of some of the designed photonic phased array switch elements is demonstrated in this chapter. An executive summary and conclusions sections are also included in the thesis.

The paradox of MHC-DRB exon/intron evolution: alpha-helix and beta-sheet encoding regions diverge while hypervariable intronic simple repeats coevolve with beta-sheet codons.

PubMed

Schwaiger, F W; Weyers, E; Epplen, C; Brün, J; Ruff, G; Crawford, A; Epplen, J T

1993-09-01

Twenty-one different caprine and 13 ovine MHC-DRB exon 2 sequences were determined including part of the adjacent introns containing simple repetitive (gt)n(ga)m elements. The positions for highly polymorphic DRB amino acids vary slightly among ungulates and other mammals. From man and mouse to ungulates the basic (gt)n(ga)m structure is fixed in evolution for 7 x 10(7) years whereas ample variations exist in the tandem (gt)n and (ga)m dinucleotides and especially their "degenerated" derivatives. Phylogenetic trees for the alpha-helices and beta-pleated sheets of the ungulate DRB sequences suggest different evolutionary histories. In hoofed animals as well as in humans DRB beta-sheet encoding sequences and adjacent intronic repeats can be assembled into virtually identical groups suggesting coevolution of noncoding as well as coding DNA. In contrast alpha-helices and C-terminal parts of the first DRB domain evolve distinctly. In the absence of a defined mechanism causing specific, site-directed mutations, double-recombination or gene-conversion-like events would readily explain this fact. The role of the intronic simple (gt)n(ga)m repeat is discussed with respect to these genetic exchange mechanisms during evolution.

A four-way junction with triple-helical arms: design, characterization, and stability.

PubMed

Makube, N; Klump, H H

2000-05-01

The formation of the four-way junction containing four triple-helical arms has been demonstrated using chemical methods (polyacrylamide gel electrophoresis and chemical footprinting using OsO(4) as a probe) and physical methods (UV absorbance melting and DSC). The junction J(T1T3) was assembled from two 20-mer purine strands and two 44-mer pyrimidine strands. To determine the contribution of the different arms to the stability of the complete structure of J(T1T3), the junction was compared to two simplified substructures, J(T1) and J(T3), respectively. Common to these complexes is the underlying double-helical four-way junction Js. Addition of Na(+) had a profound effect on stabilizing and subsequently folding the junctions into the stacked X-structures. The following results support the structure present: (i) The native polyacrylamide electrophoresis exhibits only a single band(s) corresponding to one species present when all four single strands are mixed in equal amounts. (ii) OsO(4) modifications were investigated at pH 5.0 and in the presence of 10 mM Mg(2+) and 100 mM Na(+). There is no cleavage of thymine residues at the branch point and throughout the structure. (iii) The thermal unfolding of J(T1) and J(T3) illustrates that the triple-helical arms are more stable than the double-helical arms which are contained in these junctions and that J(T1T3) with four triple-helical arms is slightly more stable than J(T1) and J(T3). (iv) The calorimetric transition enthalpies determined for the arms of J(T1T3) are comparable to those associated with the unfolding of its corresponding arms in J(T1) and J(T3). The results also illustrate that the formation of the junctions is not restricted by the pH, [Na(+)], sequence composition of the arms, and/or the loop position. Copyright 2000 Academic Press.

Robust integer and fractional helical modes in the quantum Hall effect

NASA Astrophysics Data System (ADS)

Ronen, Yuval; Cohen, Yonatan; Banitt, Daniel; Heiblum, Moty; Umansky, Vladimir

2018-04-01

Electronic systems harboring one-dimensional helical modes, where spin and momentum are locked, have lately become an important field of their own. When coupled to a conventional superconductor, such systems are expected to manifest topological superconductivity; a unique phase hosting exotic Majorana zero modes. Even more interesting are fractional helical modes, yet to be observed, which open the route for realizing generalized parafermions. Possessing non-Abelian exchange statistics, these quasiparticles may serve as building blocks in topological quantum computing. Here, we present a new approach to form protected one-dimensional helical edge modes in the quantum Hall regime. The novel platform is based on a carefully designed double-quantum-well structure in a GaAs-based system hosting two electronic sub-bands; each tuned to the quantum Hall effect regime. By electrostatic gating of different areas of the structure, counter-propagating integer, as well as fractional, edge modes with opposite spins are formed. We demonstrate that, due to spin protection, these helical modes remain ballistic over large distances. In addition to the formation of helical modes, this platform can serve as a rich playground for artificial induction of compounded fractional edge modes, and for construction of edge-mode-based interferometers.

Light-directing chiral liquid crystal nanostructures: from 1D to 3D.

PubMed

Bisoyi, Hari Krishna; Li, Quan

2014-10-21

Endowing external, remote, and dynamic control to self-organized superstructures with desired functionalities is a principal driving force in the bottom-up nanofabrication of molecular devices. Light-driven chiral molecular switches or motors in liquid crystal (LC) media capable of self-organizing into optically tunable one-dimensional (1D) and three-dimensional (3D) superstructures represent such an elegant system. As a consequence, photoresponsive cholesteric LCs (CLCs), i.e., self-organized 1D helical superstructures, and LC blue phases (BPs), i.e., self-organized 3D periodic cubic lattices, are emerging as a new generation of multifunctional supramolecular 1D and 3D photonic materials in their own right because of their fundamental academic interest and technological significance. These smart stimuli-responsive materials can be facilely fabricated from achiral LC hosts by the addition of a small amount of a light-driven chiral molecular switch or motor. The photoresponsiveness of these materials is a result of both molecular interaction and geometry changes in the chiral molecular switch upon light irradiation. The doped photoresponsive CLCs undergo light-driven pitch modulation and/or helix inversion, which has many applications in color filters, polarizers, all-optical displays, optical lasers, sensors, energy-saving smart devices, and so on. Recently, we have conceptualized and rationally synthesized different light-driven chiral molecular switches that have very high helical twisting powers (HTPs) and exhibit large changes in HTP in different states, thereby enabling wide phototunability of the systems by the addition of very small amounts of the molecular switches into commercially available achiral LCs. The light-driven chiral molecular switches are based on well-recognized azobenzene, dithienylcyclopentene, and spirooxazine derivatives. We have demonstrated high-resolution and lightweight photoaddressable displays without patterned electronics on flexible substrates. The wide tunability of the HTP furnishes reflection colors encompassing the whole visible spectrum and beyond in a reversible manner. Photomodulation of the helical pitch of the CLCs has been achieved by UV, visible, and near-infrared (NIR) light irradiation. NIR-light-induced red, green, and blue (RGB) reflections have been leveraged only by varying the power density of the IR laser. Some chiral switches are found to confer helix inversion to the cholesteric systems, which qualifies the CLCs for applications where circularly polarized light is involved. Dynamic and static primary RGB reflection colors have been achieved in a single film. LC BPs have been fabricated and investigated in the context of self-organized 3D photonic band gap (PBG) materials, and dynamic phototuning of the PBG over the visible region has been achieved. Omnidirectional lasing and tuning of the laser emission wavelength have also been attained in monodisperse photoresponsive CLC microshells fabricated by a capillary-based microfluidic technique. This Account covers the research and development in our laboratory starting from the design concepts and synthesis of photodynamic chiral molecular switches to their applications in the fabrication of photoresponsive CLCs and BPs. Potential and demonstrated practical applications of photoresponsive CLCs, microshells, and BPs are discussed, and the Account concludes with a brief forecast of what lies beyond the horizon in this rapidly expanding and fascinating field.

Dissociation of the trimeric gp41 ectodomain at the lipid-water interface suggests an active role in HIV-1 Env-mediated membrane fusion.

PubMed

Roche, Julien; Louis, John M; Grishaev, Alexander; Ying, Jinfa; Bax, Adriaan

2014-03-04

The envelope glycoprotein gp41 mediates the process of membrane fusion that enables entry of the HIV-1 virus into the host cell. The actual fusion process involves a switch from a homotrimeric prehairpin intermediate conformation, consisting of parallel coiled-coil helices, to a postfusion state where the ectodomains are arranged as a trimer of helical hairpins, adopting a six-helix bundle (6HB) state. Here, we show by solution NMR spectroscopy that a water-soluble 6HB gp41 ectodomain binds to zwitterionic detergents that contain phosphocholine or phosphatidylcholine head groups and phospholipid vesicles that mimic T-cell membrane composition. Binding results in the dissociation of the 6HB and the formation of a monomeric state, where its two α-helices, N-terminal heptad repeat (NHR) and C-terminal heptad repeat (CHR), become embedded in the lipid-water interface of the virus and host cell. The atomic structure of the gp41 ectodomain monomer, based on NOE distance restraints and residual dipolar couplings, shows that the NHR and CHR helices remain mostly intact, but they completely lose interhelical contacts. The high affinity of the ectodomain helices for phospholipid surfaces suggests that unzippering of the prehairpin intermediate leads to a state where the NHR and CHR helices become embedded in the host cell and viral membranes, respectively, thereby providing a physical force for bringing these membranes into close juxtaposition before actual fusion.

Arbitrary helicity control of circularly polarized light from lateral-type spin-polarized light-emitting diodes at room temperature

NASA Astrophysics Data System (ADS)

Nishizawa, Nozomi; Aoyama, Masaki; Roca, Ronel C.; Nishibayashi, Kazuhiro; Munekata, Hiro

2018-05-01

We demonstrate arbitrary helicity control of circularly polarized light (CPL) emitted at room temperature from the cleaved side facet of a lateral-type spin-polarized light-emitting diode (spin-LED) with two ferromagnetic electrodes in an antiparallel magnetization configuration. Driving alternate currents through the two electrodes results in polarization switching of CPL with frequencies up to 100 kHz. Furthermore, tuning the current density ratio in the two electrodes enables manipulation of the degree of circular polarization. These results demonstrate arbitrary electrical control of polarization with high speed, which is required for the practical use of lateral-type spin-LEDs as monolithic CPL light sources.

Mirrors in the PDB: left-handed alpha-turns guide design with D-amino acids.

PubMed

Annavarapu, Srinivas; Nanda, Vikas

2009-09-22

Incorporating variable amino acid stereochemistry in molecular design has the potential to improve existing protein stability and create new topologies inaccessible to homochiral molecules. The Protein Data Bank has been a reliable, rich source of information on molecular interactions and their role in protein stability and structure. D-amino acids rarely occur naturally, making it difficult to infer general rules for how they would be tolerated in proteins through an analysis of existing protein structures. However, protein elements containing short left-handed turns and helices turn out to contain useful information. Molecular mechanisms used in proteins to stabilize left-handed elements by L-amino acids are structurally enantiomeric to potential synthetic strategies for stabilizing right-handed elements with D-amino acids. Propensities for amino acids to occur in contiguous alpha(L) helices correlate with published thermodynamic scales for incorporation of D-amino acids into alpha(R) helices. Two backbone rules for terminating a left-handed helix are found: an alpha(R) conformation is disfavored at the amino terminus, and a beta(R) conformation is disfavored at the carboxy terminus. Helix capping sidechain-backbone interactions are found which are unique to alpha(L) helices including an elevated propensity for L-Asn, and L-Thr at the amino terminus and L-Gln, L-Thr and L-Ser at the carboxy terminus. By examining left-handed alpha-turns containing L-amino acids, new interaction motifs for incorporating D-amino acids into right-handed alpha-helices are identified. These will provide a basis for de novo design of novel heterochiral protein folds.

Mirrors in the PDB: left-handed α-turns guide design with D-amino acids

PubMed Central

Annavarapu, Srinivas; Nanda, Vikas

2009-01-01

Background Incorporating variable amino acid stereochemistry in molecular design has the potential to improve existing protein stability and create new topologies inaccessible to homochiral molecules. The Protein Data Bank has been a reliable, rich source of information on molecular interactions and their role in protein stability and structure. D-amino acids rarely occur naturally, making it difficult to infer general rules for how they would be tolerated in proteins through an analysis of existing protein structures. However, protein elements containing short left-handed turns and helices turn out to contain useful information. Molecular mechanisms used in proteins to stabilize left-handed elements by L-amino acids are structurally enantiomeric to potential synthetic strategies for stabilizing right-handed elements with D-amino acids. Results Propensities for amino acids to occur in contiguous αL helices correlate with published thermodynamic scales for incorporation of D-amino acids into αR helices. Two backbone rules for terminating a left-handed helix are found: an αR conformation is disfavored at the amino terminus, and a βR conformation is disfavored at the carboxy terminus. Helix capping sidechain-backbone interactions are found which are unique to αL helices including an elevated propensity for L-Asn, and L-Thr at the amino terminus and L-Gln, L-Thr and L-Ser at the carboxy terminus. Conclusion By examining left-handed α-turns containing L-amino acids, new interaction motifs for incorporating D-amino acids into right-handed α-helices are identified. These will provide a basis for de novo design of novel heterochiral protein folds. PMID:19772623

Heat Switches for ADRs

NASA Technical Reports Server (NTRS)

DiPirro, M. J.; Shirron, P. J.

2014-01-01

Heat switches are key elements in the cyclic operation of Adiabatic Demagnetization Refrigerators (ADRs). Several of the types of heat switches that have been used for ADRs are described in this paper. Key elements in selection and design of these switches include not only ON/OFF switching ratio, but also method of actuation, size, weight, and structural soundness. Some of the trade-off are detailed in this paper.

Nucleic acid nanomaterials: Silver-wired DNA

NASA Astrophysics Data System (ADS)

Auffinger, Pascal; Ennifar, Eric

2017-10-01

DNA double helical structures are supramolecular assemblies that are typically held together by classical Watson-Crick pairing. Now, nucleotide chelation of silver ions supports an extended silver-DNA hybrid duplex featuring an uninterrupted silver array.

Ras signaling requires dynamic properties of Ets1 for phosphorylation-enhanced binding to coactivator CBP.

PubMed

Nelson, Mary L; Kang, Hyun-Seo; Lee, Gregory M; Blaszczak, Adam G; Lau, Desmond K W; McIntosh, Lawrence P; Graves, Barbara J

2010-06-01

Ras/MAPK signaling is often aberrantly activated in human cancers. The downstream effectors are transcription factors, including those encoded by the ETS gene family. Using cell-based assays and biophysical measurements, we have determined the mechanism by which Ras/MAPK signaling affects the function of Ets1 via phosphorylation of Thr38 and Ser41. These ERK2 phosphoacceptors lie within the unstructured N-terminal region of Ets1, immediately adjacent to the PNT domain. NMR spectroscopic analyses demonstrated that the PNT domain is a four-helix bundle (H2-H5), resembling the SAM domain, appended with two additional helices (H0-H1). Phosphorylation shifted a conformational equilibrium, displacing the dynamic helix H0 from the core bundle. The affinity of Ets1 for the TAZ1 (or CH1) domain of the coactivator CBP was enhanced 34-fold by phosphorylation, and this binding was sensitive to ionic strength. NMR-monitored titration experiments mapped the interaction surfaces of the TAZ1 domain and Ets1, the latter encompassing both the phosphoacceptors and PNT domain. Charge complementarity of these surfaces indicate that electrostatic forces act in concert with a conformational equilibrium to mediate phosphorylation effects. We conclude that the dynamic helical elements of Ets1, appended to a conserved structural core, constitute a phospho-switch that directs Ras/MAPK signaling to downstream changes in gene expression. This detailed structural and mechanistic information will guide strategies for targeting ETS proteins in human disease.

Substituent effects in double-helical hydrogen-bonded AAA-DDD complexes.

PubMed

Wang, Hong-Bo; Mudraboyina, Bhanu P; Wisner, James A

2012-01-27

Two series of DDD and AAA hydrogen-bond arrays were synthesized that form triply-hydrogen-bonded double-helical complexes when combined in CDCl(3) solution. Derivatization of the DDD arrays with electron-withdrawing groups increases the complex association constants by up to a factor of 30 in those arrays examined. Derivatization of the AAA arrays with electron donating substituents reveals a similar magnitude effect on the complex stabilities. The effect of substitution on both types of arrays are modeled quite satisfactorily (R(2) > 0.96 in all cases) as free energy relationships with respect to the sums of their Hammett substituent constants. In all, the complex stabilities can be manipulated over more than three orders of magnitude (>20 kJ mol(-1)) using this type of modification. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Double-ended ceramic helical-rotor expander

DOEpatents

Mohr, Peter B.; Myers, Wendell B.

1995-01-01

A ceramic helical rotor expander using a double-ended or tandem herringbone type rotor arrangement with bearing and seal assemblies remote from the hot gas inlets and especially capable of operating at an inlet temperature of above 1100.degree. C. The rotors are solid or hollow and bonded to hollow metal shafts, and mounted in a composite or simple prismatic casing. The rotors, casing and shafts are constructed from low expansivity materials. In the preferred embodiment the rotors are constructed of silicon nitride and the shafts constructed of an molybdenum alloy, with the metal shafts being supported in bearings and secured to synchronizing gears. The rotors and casing may be provided with coolant channels therein, and are constructed to eliminate the problem of end leakages at inlet temperature and pressure, and the need for high temperature bearings and seals.

Double-ended ceramic helical-rotor expander

DOEpatents

Mohr, P.B.; Myers, W.B.

1995-02-28

A ceramic helical rotor expander is disclosed using a double-ended or tandem herringbone type rotor arrangement with bearing and seal assemblies remote from the hot gas inlets and especially capable of operating at an inlet temperature of above 1,100 C. The rotors are solid or hollow and bonded to hollow metal shafts, and mounted in a composite or simple prismatic casing. The rotors, casing and shafts are constructed from low expansivity materials. In the preferred embodiment the rotors are constructed of silicon nitride and the shafts constructed of an molybdenum alloy, with the metal shafts being supported in bearings and secured to synchronizing gears. The rotors and casing may be provided with coolant channels therein, and are constructed to eliminate the problem of end leakages at inlet temperature and pressure, and the need for high temperature bearings and seals. 3 figs.

Measurements of double-helicity asymmetries in inclusive J / ψ production in longitudinally polarized p + p collisions at s = 510 GeV

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

Adare, A.; Aidala, C.; Ajitanand, N. N.

We report the double-helicity asymmetry, A J/ψ LL, in inclusive J/ψ production at forward rapidity as a function of transverse momentum p T and rapidity |y|. The data analyzed were taken during √s = 510 GeV longitudinally polarized p + p collisions at the Relativistic Heavy Ion Collider in the 2013 run using the PHENIX detector. At this collision energy, J/ψ particles are predominantly produced through gluon-gluon scatterings, thus A J/ψ LL is sensitive to the gluon polarization inside the proton. We measured A J/ψ LL by detecting the decay daughter muon pairs μ +μ – within the PHENIX muonmore » spectrometers in the rapidity range 1.2 < |y| < 2.2. In this kinematic range, we measured the A J/ψ LL to be 0.012 ± 0.010 (stat) ±0.003 (syst). The A J/ψ LL can be expressed to be proportional to the product of the gluon polarization distributions at two distinct ranges of Bjorken x: one at moderate range x ≈ 5 × 10 –2 where recent data of jet and π 0 double helicity spin asymmetries have shown evidence for significant gluon polarization, and the other one covering the poorly known small-x region x ≈ 2 × 10 –3. Furthermore, our new results could be used to further constrain the gluon polarization for x < 5 × 10 –2.« less

Measurements of double-helicity asymmetries in inclusive J / ψ production in longitudinally polarized p + p collisions at s = 510 GeV

DOE PAGES

Adare, A.; Aidala, C.; Ajitanand, N. N.; ...

2016-12-29

We report the double-helicity asymmetry, A J/ψ LL, in inclusive J/ψ production at forward rapidity as a function of transverse momentum p T and rapidity |y|. The data analyzed were taken during √s = 510 GeV longitudinally polarized p + p collisions at the Relativistic Heavy Ion Collider in the 2013 run using the PHENIX detector. At this collision energy, J/ψ particles are predominantly produced through gluon-gluon scatterings, thus A J/ψ LL is sensitive to the gluon polarization inside the proton. We measured A J/ψ LL by detecting the decay daughter muon pairs μ +μ – within the PHENIX muonmore » spectrometers in the rapidity range 1.2 < |y| < 2.2. In this kinematic range, we measured the A J/ψ LL to be 0.012 ± 0.010 (stat) ±0.003 (syst). The A J/ψ LL can be expressed to be proportional to the product of the gluon polarization distributions at two distinct ranges of Bjorken x: one at moderate range x ≈ 5 × 10 –2 where recent data of jet and π 0 double helicity spin asymmetries have shown evidence for significant gluon polarization, and the other one covering the poorly known small-x region x ≈ 2 × 10 –3. Furthermore, our new results could be used to further constrain the gluon polarization for x < 5 × 10 –2.« less

Vortex operation in Er:LuYAG crystal laser at ∼1.6 μm

NASA Astrophysics Data System (ADS)

Liu, Qiyao; Zhao, Yongguang; Zhou, Wei; Shen, Deyuan

2017-09-01

An Er3+-doped Lu1.5Y1.5Al5O12 (Er:LuYAG) solid-state laser with direct generation of optical vortex is reported. The vortex laser operation was realized through being pumped by an annular beam at 1532 nm, which was reformatted by a specially fabricated optical mirror. With two different laser output couplers of 10% and 20% transmissions, pure LG01 mode lasers with right-handedness at 1647.7 nm and 1619.5 nm were yielded from a simple two-mirror cavity, respectively, without any helicity control optical element. Furthermore, stable pulse trains at 1647.7 nm have been achieved via employing an acousto-optic Q-switch, and ∼0.66 mJ pulsed energy and ∼65 ns pulse duration were finally obtained at 1 kHz repetition rate, corresponding to a peak power of ∼10.2 kW. The generated pulse vortex maintained LG01 mode with well-determined right-handedness, as in the case of cw laser operation.

A new very high voltage semiconductor switch

NASA Technical Reports Server (NTRS)

Sundberg, G. R.

1985-01-01

A new family of semiconductor switches using double injection techniques and compensated deep impurities is described. They have the potential to raise switching voltages a factor of 10 higher (up to 100 kV) than p-n junction devices while exhibiting extremely low (or zero) forward voltage. Several potential power switching applications are indicated.

All-optical spin switching: A new frontier in femtomagnetism — A short review and a simple theory

NASA Astrophysics Data System (ADS)

Zhang, G. P.; Latta, T.; Babyak, Z.; Bai, Y. H.; George, Thomas F.

2016-08-01

Using an ultrafast laser pulse to manipulate the spin degree of freedom has broad technological appeal. It allows one to control the spin dynamics on a femtosecond time scale. The discipline, commonly called femtomagnetism, started with the pioneering experiment by Beaurepaire and coworkers in 1996, who showed subpicosecond demagnetization occurs in magnetic Ni thin films. This finding has motivated extensive research worldwide. All-optical helicity-dependent spin switching (AO-HDS) represents a new frontier in femtomagnetism, where a single ultrafast laser pulse can permanently switch spin without any assistance from a magnetic field. This review summarizes some of the crucial aspects of this new discipline: key experimental findings, leading mechanisms, controversial issues, and possible future directions. The emphasis is on our latest investigation. We first develop the all-optical spin switching (AOS) rule that determines how the switchability depends on the light helicity. This rule allows one to understand microscopically how the spin is reversed and why the circularly polarized light appears more powerful than the linearly polarized light. Then we invoke our latest spin-orbit coupled harmonic oscillator model to simulate single spin reversal. We consider both continuous wave (cw) excitation and pulsed laser excitation. The results are in a good agreement with the experimental result (a MatLab code is available upon request from the author). We then extend the code to include the exchange interaction among different spin sites. We show where the “inverse-Faraday field” comes from and how the laser affects the spin reversal nonlinearly. Our hope is that this review will motivate new experimental and theoretical investigations and discussions.

Beam-Helicity Asymmetries in Double-Charged-Pion Photoproduction on the Proton

NASA Astrophysics Data System (ADS)

Strauch, S.; Berman, B. L.; Adams, G.; Ambrozewicz, P.; Anghinolfi, M.; Asavapibhop, B.; Asryan, G.; Audit, G.; Avakian, H.; Bagdasaryan, H.; Baillie, N.; Ball, J. P.; Baltzell, N. A.; Barrow, S.; Batourine, V.; Battaglieri, M.; Beard, K.; Bedlinskiy, I.; Bektasoglu, M.; Bellis, M.; Benmouna, N.; Bennhold, C.; Biselli, A. S.; Boiarinov, S.; Bouchigny, S.; Bradford, R.; Branford, D.; Briscoe, W. J.; Brooks, W. K.; Bültmann, S.; Burkert, V. D.; Butuceanu, C.; Calarco, J. R.; Careccia, S. L.; Carman, D. S.; Carnahan, B.; Chen, S.; Cole, P. L.; Coleman, A.; Coltharp, P.; Cords, D.; Corvisiero, P.; Crabb, D.; Crannell, H.; Cummings, J. P.; Degtyarenko, P. V.; Denizli, H.; Dennis, L.; de Sanctis, E.; Deur, A.; Devita, R.; Dharmawardane, K. V.; Dhuga, K. S.; Djalali, C.; Dodge, G. E.; Donnelly, J.; Doughty, D.; Dragovitsch, P.; Dugger, M.; Dytman, S.; Dzyubak, O. P.; Egiyan, H.; Egiyan, K. S.; Elouadrhiri, L.; Empl, A.; Eugenio, P.; Fatemi, R.; Fedotov, G.; Feldman, G.; Feuerbach, R. J.; Fix, A.; Forest, T. A.; Funsten, H.; Gavalian, G.; Gilfoyle, G. P.; Giovanetti, K. L.; Girod, F. X.; Goetz, J. T.; Gothe, R. W.; Griffioen, K. A.; Guidal, M.; Guler, N.; Guo, L.; Gyurjyan, V.; Hadjidakis, C.; Hakobyan, R. S.; Hardie, J.; Heddle, D.; Hersman, F. W.; Hicks, K.; Hleiqawi, I.; Holtrop, M.; Hu, J.; Huertas, M.; Hyde-Wright, C. E.; Ilieva, Y.; Ireland, D. G.; Ishkhanov, B. S.; Ito, M. M.; Jenkins, D.; Jo, H. S.; Joo, K.; Juengst, H. G.; Kellie, J. D.; Khandaker, M.; Kim, K. Y.; Kim, K.; Kim, W.; Klein, A.; Klein, F. J.; Klimenko, A. V.; Klusman, M.; Kossov, M.; Kramer, L. H.; Kubarovsky, V.; Kuhn, J.; Kuhn, S. E.; Lachniet, J.; Laget, J. M.; Langheinrich, J.; Lawrence, D.; Lee, T.; Lima, A. C. S.; Livingston, K.; Lukashin, K.; Manak, J. J.; Marchand, C.; McAleer, S.; McKinnon, B.; McNabb, J. W. C.; Mecking, B. A.; Mestayer, M. D.; Meyer, C. A.; Mibe, T.; Mikhailov, K.; Minehart, R.; Mirazita, M.; Miskimen, R.; Mokeev, V.; Morrow, S. A.; Muccifora, V.; Mueller, J.; Mutchler, G. S.; Nadel-Turonski, P.; Napolitano, J.; Nasseripour, R.; Niccolai, S.; Niculescu, G.; Niculescu, I.; Niczyporuk, B. B.; Niyazov, R. A.; Nozar, M.; O'Rielly, G. V.; Osipenko, M.; Ostrovidov, A. I.; Park, K.; Pasyuk, E.; Paterson, C.; Philips, S. A.; Pierce, J.; Pivnyuk, N.; Pocanic, D.; Pogorelko, O.; Polli, E.; Pozdniakov, S.; Preedom, B. M.; Price, J. W.; Prok, Y.; Protopopescu, D.; Qin, L. M.; Raue, B. A.; Riccardi, G.; Ricco, G.; Ripani, M.; Ritchie, B. G.; Roberts, W.; Ronchetti, F.; Rosner, G.; Rossi, P.; Rowntree, D.; Rubin, P. D.; Sabatié, F.; Salgado, C.; Santoro, J. P.; Sapunenko, V.; Schumacher, R. A.; Serov, V. S.; Shafi, A.; Sharabian, Y. G.; Shaw, J.; Skabelin, A. V.; Smith, E. S.; Smith, L. C.; Sober, D. I.; Stavinsky, A.; Stepanyan, S. S.; Stepanyan, S.; Stokes, B. E.; Stoler, P.; Strakovsky, I. I.; Suleiman, R.; Taiuti, M.; Taylor, S.; Tedeschi, D. J.; Thoma, U.; Thompson, R.; Tkabladze, A.; Tkachenko, S.; Todor, L.; Tur, C.; Ungaro, M.; Vineyard, M. F.; Vlassov, A. V.; Wang, K.; Weinstein, L. B.; Weygand, D. P.; Williams, M.; Wolin, E.; Wood, M. H.; Yegneswaran, A.; Yun, J.; Zana, L.; Zhang, J.

2005-10-01

Beam-helicity asymmetries for the two-pion-photoproduction reaction γ→p→pπ+π- have been studied for the first time in the resonance region for center-of-mass energies between 1.35 and 2.30 GeV. The experiment was performed at Jefferson Lab with the CEBAF Large Acceptance Spectrometer using circularly polarized tagged photons incident on an unpolarized hydrogen target. Beam-helicity-dependent angular distributions of the final-state particles were measured. The large cross-section asymmetries exhibit strong sensitivity to the kinematics and dynamics of the reaction. The data are compared with the results of various phenomenological model calculations, and show that these models currently do not provide an adequate description for the behavior of this new observable.

A CW Gunn Diode Switching Element.

ERIC Educational Resources Information Center

Hurtado, Marco; Rosenbaum, Fred J.

As part of a study of the application of communication satellites to educational development, certain technical aspects of such a system were examined. A current controlled bistable switching element using a CW Gunn diode is reported on here. With modest circuits switching rates of the order of 10 MHz have been obtained. Switching is initiated by…

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

Mei, Yang; Ramanathan, Arvind; Glover, Karen

BECN1 is essential for autophagy, a critical eukaryotic cellular homeostasis pathway. Here we delineate a highly conserved BECN1 domain located between previously characterized BH3 and coiled-coil domains and elucidate its structure and role in autophagy. The 2.0 angstrom sulfur-single-wavelength anomalous dispersion X-ray crystal structure of this domain demonstrates that its N-terminal half is unstructured while its C-terminal half is helical; hence, we name it the flexible helical domain (FHD). Circular dichroism spectroscopy, double electron electron resonance electron paramagnetic resonance, and small-angle X-ray scattering (SAXS) analyses confirm that the FHD is partially disordered, even in the context of adjacent BECN1 domains.more » Molecular dynamic simulations fitted to SAXS data indicate that the FHD transiently samples more helical conformations. FHD helicity increases in 2,2,2-trifluoroethanol, suggesting it may become more helical upon binding. Lastly, cellular studies show that conserved FHD residues are required for starvation-induced autophagy. Thus, the FHD likely undergoes a binding-associated disorder to-helix transition, and conserved residues critical for this interaction are essential for starvation-induced autophagy.« less

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

Mei, Yang; Ramanathan, Arvind; Glover, Karen

BECN1 is essential for autophagy, a critical eukaryotic cellular homeostasis pathway. Here in this study, we delineate a highly conserved BECN1 domain located between previously characterized BH3 and coiled-coil domains and elucidate its structure and role in autophagy. The 2.0 Å sulfur-single-wavelength anomalous dispersion X-ray crystal structure of this domain demonstrates that its N-terminal half is unstructured while its C-terminal half is helical; hence, we name it the flexible helical domain (FHD). Circular dichroism spectroscopy, double electron–electron resonance–electron paramagnetic resonance, and small-angle X-ray scattering (SAXS) analyses confirm that the FHD is partially disordered, even in the context of adjacent BECN1more » domains. Molecular dynamic simulations fitted to SAXS data indicate that the FHD transiently samples more helical conformations. FHD helicity increases in 2,2,2-trifluoroethanol, suggesting it may become more helical upon binding. Finally, cellular studies show that conserved FHD residues are required for starvation-induced autophagy. Thus, the FHD likely undergoes a binding-associated disorder-to-helix transition, and conserved residues critical for this interaction are essential for starvation-induced autophagy.« less

Three New Structures of Left-Handed RadA Helical Filaments: Structural Flexibility of N-Terminal Domain Is Critical for Recombinase Activity

PubMed Central

Chang, Yu-Wei; Ko, Tzu-Ping; Lee, Chien-Der; Chang, Yuan-Chih; Lin, Kuei-Ann; Chang, Chia-Seng; Wang, Andrew H.-J.; Wang, Ting-Fang

2009-01-01

RecA family proteins, including bacterial RecA, archaeal RadA, and eukaryotic Dmc1 and Rad51, mediate homologous recombination, a reaction essential for maintaining genome integrity. In the presence of ATP, these proteins bind a single-strand DNA to form a right-handed nucleoprotein filament, which catalyzes pairing and strand exchange with a homologous double-stranded DNA (dsDNA), by as-yet unknown mechanisms. We recently reported a structure of RadA left-handed helical filament, and here present three new structures of RadA left-handed helical filaments. Comparative structural analysis between different RadA/Rad51 helical filaments reveals that the N-terminal domain (NTD) of RadA/Rad51, implicated in dsDNA binding, is highly flexible. We identify a hinge region between NTD and polymerization motif as responsible for rigid body movement of NTD. Mutant analysis further confirms that structural flexibility of NTD is essential for RadA's recombinase activity. These results support our previous hypothesis that ATP-dependent axial rotation of RadA nucleoprotein helical filament promotes homologous recombination. PMID:19295907

Formation of template-switching artifacts by linear amplification.

PubMed

Chakravarti, Dhrubajyoti; Mailander, Paula C

2008-07-01

Linear amplification is a method of synthesizing single-stranded DNA from either a single-stranded DNA or one strand of a double-stranded DNA. In this protocol, molecules of a single primer DNA are extended by multiple rounds of DNA synthesis at high temperature using thermostable DNA polymerases. Although linear amplification generates the intended full-length single-stranded product, it is more efficient over single-stranded templates than double-stranded templates. We analyzed linear amplification over single- or double-stranded mouse H-ras DNA (exon 1-2 region). The single-stranded H-ras template yielded only the intended product. However, when the double-stranded template was used, additional artifact products were observed. Increasing the concentration of the double-stranded template produced relatively higher amounts of these artifact products. One of the artifact DNA bands could be mapped and analyzed by sequencing. It contained three template-switching products. These DNAs were formed by incomplete DNA strand extension over the template strand, followed by switching to the complementary strand at a specific Ade nucleotide within a putative hairpin sequence, from which DNA synthesis continued over the complementary strand.

Structural basis for diversity in the SAM clan of riboswitches.

PubMed

Trausch, Jeremiah J; Xu, Zhenjiang; Edwards, Andrea L; Reyes, Francis E; Ross, Phillip E; Knight, Rob; Batey, Robert T

2014-05-06

In bacteria, sulfur metabolism is regulated in part by seven known families of riboswitches that bind S-adenosyl-l-methionine (SAM). Direct binding of SAM to these mRNA regulatory elements governs a downstream secondary structural switch that communicates with the transcriptional and/or translational expression machinery. The most widely distributed SAM-binding riboswitches belong to the SAM clan, comprising three families that share a common SAM-binding core but differ radically in their peripheral architecture. Although the structure of the SAM-I member of this clan has been extensively studied, how the alternative peripheral architecture of the other families supports the common SAM-binding core remains unknown. We have therefore solved the X-ray structure of a member of the SAM-I/IV family containing the alternative "PK-2" subdomain shared with the SAM-IV family. This structure reveals that this subdomain forms extensive interactions with the helix housing the SAM-binding pocket, including a highly unusual mode of helix packing in which two helices pack in a perpendicular fashion. Biochemical and genetic analysis of this RNA reveals that SAM binding induces many of these interactions, including stabilization of a pseudoknot that is part of the regulatory switch. Despite strong structural similarity between the cores of SAM-I and SAM-I/IV members, a phylogenetic analysis of sequences does not indicate that they derive from a common ancestor.

Electric heater for nuclear fuel rod simulators

DOEpatents

McCulloch, Reginald W.; Morgan, Jr., Chester S.; Dial, Ralph E.

1982-01-01

The present invention is directed to an electric cartridge-type heater for use as a simulator for a nuclear fuel pin in reactor studies. The heater comprises an elongated cylindrical housing containing a longitudinally extending helically wound heating element with the heating element radially inwardly separated from the housing. Crushed cold-pressed preforms of boron nitride electrically insulate the heating element from the housing while providing good thermal conductivity. Crushed cold-pressed preforms of magnesia or a magnesia-15 percent boron nitride mixture are disposed in the cavity of the helical heating element. The coefficient of thermal expansion of the magnesia or the magnesia-boron nitride mixture is higher than that of the boron nitride disposed about the heating element for urging the boron nitride radially outwardly against the housing during elevated temperatures to assure adequate thermal contact between the housing and the boron nitride.

Influence of a change in helical twisting power of photoresponsive chiral dopants on rotational manipulation of micro-objects on the surface of chiral nematic liquid crystalline films.

PubMed

Thomas, Reji; Yoshida, Yohei; Akasaka, Takehito; Tamaoki, Nobuyuki

2012-09-24

Herein we report a group of five planar chiral molecules as photon-mode chiral switches for the reversible control of the self-assembled superstructures of doped chiral nematic liquid crystals. The chiral switches are composed of an asymmetrically substituted aromatic moiety and a photoisomerizing azobenzene unit connected in a cyclic manner through methylene spacers of varying lengths. All the molecules show conformational restriction in the rotation of the asymmetrically substituted aromatic moiety in both the E and Z states of the azobenzene units resulting in planar chirality with separable enantiomers. Our newly synthesized compounds in pure enantiomeric form show high helical twisting power (HTP) in addition to an improved change in HTP between the E and Z states. The molecule with a diphenylnaphthalene unit shows the highest ever known initial helical twisting power among chiral dopants with planar chirality. In addition to the reversible tuning of reflection colors, we employed the enantiomers of these five compounds in combination with four nematic liquid crystalline hosts to study their properties as molecular machines; the change in HTP of the chiral dopant upon photoisomerization induces rotation of the texture of the liquid crystal surfaces. Importantly, this study has revealed a linear dependence of the ratio of the difference between HTPs before and after irradiation against the absolute value of the initial HTP, not the absolute value of the change in helical twisting power between two states, on the angle of rotation of micro-objects on chiral nematic liquid crystalline films. This study has also revealed that a change in irradiation intensity does not affect the maximum angle of rotation, but it does affect the speed of rotational reorganization of the cholesteric helix. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sequence-dependent folding landscapes of adenine riboswitch aptamers.

PubMed

Lin, Jong-Chin; Hyeon, Changbong; Thirumalai, D

2014-04-14

Expression of a large fraction of genes in bacteria is controlled by riboswitches, which are found in the untranslated region of mRNA. Structurally riboswitches have a conserved aptamer domain to which a metabolite binds, resulting in a conformational change in the downstream expression platform. Prediction of the functions of riboswitches requires a quantitative description of the folding landscape so that the barriers and time scales for the conformational change in the switching region in the aptamer can be estimated. Using a combination of all atom molecular dynamics (MD) and coarse-grained model simulations we studied the response of adenine (A) binding add and pbuE A-riboswitches to mechanical force. The two riboswitches contain a structurally similar three-way junction formed by three paired helices, P1, P2, and P3, but carry out different functions. Using pulling simulations, with structures generated in MD simulations, we show that after P1 rips the dominant unfolding pathway in the add A-riboswitch is the rupture of P2 followed by unraveling of P3. In the pbuE A-riboswitch, after P1 unfolds P3 ruptures ahead of P2. The order of unfolding of the helices, which is in accord with single molecule pulling experiments, is determined by the relative stabilities of the individual helices. Our results show that the stability of isolated helices determines the order of assembly and response to force in these non-coding regions. We use the simulated free energy profile for the pbuE A-riboswitch to estimate the time scale for allosteric switching, which shows that this riboswitch is under kinetic control lending additional support to the conclusion based on single molecule pulling experiments. A consequence of the stability hypothesis is that a single point mutation (U28C) in the P2 helix of the add A-riboswitch, which increases the stability of P2, would make the folding landscapes of the two riboswitches similar. This prediction can be tested in single molecule pulling experiments.

Secbase: database module to retrieve secondary structure elements with ligand binding motifs.

PubMed

Koch, Oliver; Cole, Jason; Block, Peter; Klebe, Gerhard

2009-10-01

Secbase is presented as a novel extension module of Relibase. It integrates the information about secondary structure elements into the retrieval facilities of Relibase. The data are accessible via the extended Relibase user interface, and integrated retrieval queries can be addressed using an extended version of Reliscript. The primary information about alpha-helices and beta-sheets is used as provided by the PDB. Furthermore, a uniform classification of all turn families, based on recent clustering methods, and a new helix assignment that is based on this turn classification has been included. Algorithms to analyze the geometric features of helices and beta-strands were also implemented. To demonstrate the performance of the Secbase implementation, some application examples are given. They provide new insights into the involvement of secondary structure elements in ligand binding. A survey of water molecules detected next to the N-terminus of helices is analyzed to show their involvement in ligand binding. Additionally, the parallel oriented NH groups at the alpha-helix N-termini provide special binding motifs to bind particular ligand functional groups with two adjacent oxygen atoms, e.g., as found in negatively charged carboxylate or phosphate groups, respectively. The present study also shows that the specific structure of the first turn of alpha-helices provides a suitable explanation for stabilizing charged structures. The magnitude of the overall helix macrodipole seems to have no or only a minor influence on binding. Furthermore, an overview of the involvement of secondary structure elements with the recognition of some important endogenous ligands such as cofactors shows some distinct preference for particular binding motifs and amino acids.

Proline Scanning Mutagenesis Reveals a Role for the Flap Endonuclease-1 Helical Cap in Substrate Unpairing*

PubMed Central

Patel, Nikesh; Exell, Jack C.; Jardine, Emma; Ombler, Ben; Finger, L. David; Ciani, Barbara; Grasby, Jane A.

2013-01-01

The prototypical 5′-nuclease, flap endonuclease-1 (FEN1), catalyzes the essential removal of single-stranded flaps during DNA replication and repair. FEN1 hydrolyzes a specific phosphodiester bond one nucleotide into double-stranded DNA. This specificity arises from double nucleotide unpairing that places the scissile phosphate diester on active site divalent metal ions. Also related to FEN1 specificity is the helical arch, through which 5′-flaps, but not continuous DNAs, can thread. The arch contains basic residues (Lys-93 and Arg-100 in human FEN1 (hFEN1)) that are conserved by all 5′-nucleases and a cap region only present in enzymes that process DNAs with 5′ termini. Proline mutations (L97P, L111P, L130P) were introduced into the hFEN1 helical arch. Each mutation was severely detrimental to reaction. However, all proteins were at least as stable as wild-type (WT) hFEN1 and bound substrate with comparable affinity. Moreover, all mutants produced complexes with 5′-biotinylated substrate that, when captured with streptavidin, were resistant to challenge with competitor DNA. Removal of both conserved basic residues (K93A/R100A) was no more detrimental to reaction than the single mutation R100A, but much less severe than L97P. The ability of protein-Ca2+ to rearrange 2-aminopurine-containing substrates was monitored by low energy CD. Although L97P and K93A/R100A retained the ability to unpair substrates, the cap mutants L111P and L130P did not. Taken together, these data challenge current assumptions related to 5′-nuclease family mechanism. Conserved basic amino acids are not required for double nucleotide unpairing and appear to act cooperatively, whereas the helical cap plays an unexpected role in hFEN1-substrate rearrangement. PMID:24126913

A hybrid deterministic-probabilistic approach to model the mechanical response of helically arranged hierarchical strands

NASA Astrophysics Data System (ADS)

Fraldi, M.; Perrella, G.; Ciervo, M.; Bosia, F.; Pugno, N. M.

2017-09-01

Very recently, a Weibull-based probabilistic strategy has been successfully applied to bundles of wires to determine their overall stress-strain behaviour, also capturing previously unpredicted nonlinear and post-elastic features of hierarchical strands. This approach is based on the so-called "Equal Load Sharing (ELS)" hypothesis by virtue of which, when a wire breaks, the load acting on the strand is homogeneously redistributed among the surviving wires. Despite the overall effectiveness of the method, some discrepancies between theoretical predictions and in silico Finite Element-based simulations or experimental findings might arise when more complex structures are analysed, e.g. helically arranged bundles. To overcome these limitations, an enhanced hybrid approach is proposed in which the probability of rupture is combined with a deterministic mechanical model of a strand constituted by helically-arranged and hierarchically-organized wires. The analytical model is validated comparing its predictions with both Finite Element simulations and experimental tests. The results show that generalized stress-strain responses - incorporating tension/torsion coupling - are naturally found and, once one or more elements break, the competition between geometry and mechanics of the strand microstructure, i.e. the different cross sections and helical angles of the wires in the different hierarchical levels of the strand, determines the no longer homogeneous stress redistribution among the surviving wires whose fate is hence governed by a "Hierarchical Load Sharing" criterion.

Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism.

PubMed

Samatey, Fadel A; Matsunami, Hideyuki; Imada, Katsumi; Nagashima, Shigehiro; Shaikh, Tanvir R; Thomas, Dennis R; Chen, James Z; Derosier, David J; Kitao, Akio; Namba, Keiichi

2004-10-28

The bacterial flagellum is a motile organelle, and the flagellar hook is a short, highly curved tubular structure that connects the flagellar motor to the long filament acting as a helical propeller. The hook is made of about 120 copies of a single protein, FlgE, and its function as a nano-sized universal joint is essential for dynamic and efficient bacterial motility and taxis. It transmits the motor torque to the helical propeller over a wide range of its orientation for swimming and tumbling. Here we report a partial atomic model of the hook obtained by X-ray crystallography of FlgE31, a major proteolytic fragment of FlgE lacking unfolded terminal regions, and by electron cryomicroscopy and three-dimensional helical image reconstruction of the hook. The model reveals the intricate molecular interactions and a plausible switching mechanism for the hook to be flexible in bending but rigid against twisting for its universal joint function.

Reversible near-infrared light directed reflection in a self-organized helical superstructure loaded with upconversion nanoparticles.

PubMed

Wang, Ling; Dong, Hao; Li, Yannian; Xue, Chenming; Sun, Ling-Dong; Yan, Chun-Hua; Li, Quan

2014-03-26

Adding external, dynamic control to self-organized superstructures with desired functionalities is an important leap necessary in leveraging the fascinating molecular systems for applications. Here, the new light-driven chiral molecular switch and upconversion nanoparticles, doped in a liquid crystal media, were able to self-organize into an optically tunable helical superstructure. The resulting nanoparticle impregnated helical superstructure was found to exhibit unprecedented reversible near-infrared (NIR) light-guided tunable behavior only by modulating the excitation power density of a continuous-wave NIR laser (980 nm). Upon irradiation by the NIR laser at the high power density, the reflection wavelength of the photonic superstructure red-shifted, whereas its reverse process occurred upon irradiation by the same laser but with the lower power density. Furthermore, reversible dynamic NIR-light-driven red, green, and blue reflections in a single thin film, achieved only by varying the power density of the NIR light, were for the first time demonstrated.

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.

Structural Plasticity of Helical Nanotubes Based on Coiled-Coil Assemblies

DOE PAGES

Egelman, Edward H.; Xu, C.; DiMaio, F.; ...

2015-01-22

Numerous instances can be seen in evolution in which protein quaternary structures have diverged while the sequences of the building blocks have remained fairly conserved. However, the path through which such divergence has taken place is usually not known. We have designed two synthetic 29-residue α-helical peptides, based on the coiled-coil structural motif, that spontaneously self-assemble into helical nanotubes in vitro. Using electron cryomicroscopy with a newly available direct electron detection capability, we can achieve near-atomic resolution of these thin structures. We show how conservative changes of only one or two amino acids result in dramatic changes in quaternary structure,more » in which the assemblies can be switched between two very different forms. This system provides a framework for understanding how small sequence changes in evolution can translate into very large changes in supramolecular structure, a phenomenon that may have significant implications for the de novo design of synthetic peptide assemblies.« less

Mechanical properties of DNA-like polymers

PubMed Central

Peters, Justin P.; Yelgaonkar, Shweta P.; Srivatsan, Seergazhi G.; Tor, Yitzhak; James Maher, L.

2013-01-01

The molecular structure of the DNA double helix has been known for 60 years, but we remain surprisingly ignorant of the balance of forces that determine its mechanical properties. The DNA double helix is among the stiffest of all biopolymers, but neither theory nor experiment has provided a coherent understanding of the relative roles of attractive base stacking forces and repulsive electrostatic forces creating this stiffness. To gain insight, we have created a family of double-helical DNA-like polymers where one of the four normal bases is replaced with various cationic, anionic or neutral analogs. We apply DNA ligase-catalyzed cyclization kinetics experiments to measure the bending and twisting flexibilities of these polymers under low salt conditions. Interestingly, we show that these modifications alter DNA bending stiffness by only 20%, but have much stronger (5-fold) effects on twist flexibility. We suggest that rather than modifying DNA stiffness through a mechanism easily interpretable as electrostatic, the more dominant effect of neutral and charged base modifications is their ability to drive transitions to helical conformations different from canonical B-form DNA. PMID:24013560

Electrostatic Interactions Mediate Binding of Obscurin to Small Ankyrin 1: Biochemical and Molecular Modeling Studies

PubMed Central

Busby, Ben; Oashi, Taiji; Willis, Chris D.; Ackermann, Maegen A.; Kontrogianni-Konstantopoulos, Aikaterini; MacKerell, Alexander D.; Bloch, Robert J.

2012-01-01

Small ankyrin 1 (sAnk1; also Ank1.5) is an integral protein of the sarcoplasmic reticulum in skeletal and cardiac muscle cells, where it is thought to bind to the C-terminal region of obscurin, a large modular protein that surrounds the contractile apparatus. Using fusion proteins in vitro, in combination with site directed mutagenesis and surface plasmon resonance measurements, we previously showed that the binding site on sAnk1 for obscurin consists in part of six lysine and arginine residues. Here we show that four charged residues in the high affinity binding site on obscurin for sAnk1, between residues 6316-6345, consisting of three glutamates and a lysine, are necessary, but not sufficient, for this site on obscurin to bind with high affinity to sAnk1. We also identify specific complementary mutations in sAnk1 that can partially or completely compensate for the changes in binding caused by charge-switching mutations in obscurin. We used molecular modeling to develop structural models of residues 6322-6339 of obscurin bound to sAnk1. The models, based on a combination of Brownian and molecular dynamics simulations, predict that the binding site on sAnk1 for obscurin is organized as two ankyrin-like repeats, with the last α-helical segment oriented at an angle to the nearby helices, allowing lysine-6338 of obscurin to form an ionic interaction with aspartate-111 of sAnk1. This prediction was validated by double mutant cycle experiments. Our results are consistent with a model in which electrostatic interactions between specific pairs of side chains on obscurin and sAnk1 promote binding and complex formation. PMID:21333652

Towards a Predictive Capability for Local Helicity Injection Startup

NASA Astrophysics Data System (ADS)

Barr, J. L.; Bongard, M. W.; Burke, M. G.; Fonck, R. J.; Hinson, E. T.; Lewicki, B. T.; Perry, J. M.; Redd, A. J.; Schlossberg, D. J.

2014-10-01

Local helicity injection (LHI) is a non-solenoidal tokamak startup technique under development on the Pegasus ST. New designs of the injector cathode geometry and plasma-facing shield rings support high-voltage operation up to 1.5 kV. This leads to reduced requirements in injector area for a given helicity input rate. Near-term experiments in Pegasus are testing the gain in Ip obtained with a 1 . 5 × increase in the helicity input rate and the efficacy of helicity injection in the lower divertor region. A predictive model for LHI is needed to project scalable scenarios for larger devices. A lumped-parameter circuit model using power and helicity balance is being developed for LHI on Pegasus-U and NSTX-U. The model indicates that MA-class startup on NSTX-U will require operating in a regime where the drive from LHI dominates the inductive effects arising from dynamically evolving plasma geometry. The physics of this new regime can be tested in Pegasus-U at Ip ~ 0 . 3 MA. The LHI systems on the proposed Pegasus-U will be expanded to provide 3 - 4 × helicity injection rate and the toroidal field doubled to reach this regime. Predictive models to be validated on Pegasus-U include the 0-D power balance model, NIMROD, and TSC. Work supported by US DOE Grants DE-FG02-96ER54375 and DE-SC0006928.

Stereochemical model for proflavin intercalation in A-DNA.

PubMed Central

Alden, C J; Arnott, S

1977-01-01

Linked-atom molecular modelling was employed to determine the steric and torsional requirements for intercalation of proflavine into a double-stranded region of DNA compatible with adjacent regions of cohelical A-DNA. The optimum intercalation conformation is characterized by the dihedral angles xi and psi becoming trans, with all sugars retaining the characteristics C3'-endo pucker. This extended conformation results in virtually no helical unwinding, suggesting it may be an appropriate model for an intercalative intermediary in mutagenesis by virtue of its similarity to standard helical DNA. PMID:593890

Switching algorithm for maglev train double-modular redundant positioning sensors.

PubMed

He, Ning; Long, Zhiqiang; Xue, Song

2012-01-01

High-resolution positioning for maglev trains is implemented by detecting the tooth-slot structure of the long stator installed along the rail, but there are large joint gaps between long stator sections. When a positioning sensor is below a large joint gap, its positioning signal is invalidated, thus double-modular redundant positioning sensors are introduced into the system. This paper studies switching algorithms for these redundant positioning sensors. At first, adaptive prediction is applied to the sensor signals. The prediction errors are used to trigger sensor switching. In order to enhance the reliability of the switching algorithm, wavelet analysis is introduced to suppress measuring disturbances without weakening the signal characteristics reflecting the stator joint gap based on the correlation between the wavelet coefficients of adjacent scales. The time delay characteristics of the method are analyzed to guide the algorithm simplification. Finally, the effectiveness of the simplified switching algorithm is verified through experiments.

Switching Algorithm for Maglev Train Double-Modular Redundant Positioning Sensors

PubMed Central

He, Ning; Long, Zhiqiang; Xue, Song

2012-01-01

High-resolution positioning for maglev trains is implemented by detecting the tooth-slot structure of the long stator installed along the rail, but there are large joint gaps between long stator sections. When a positioning sensor is below a large joint gap, its positioning signal is invalidated, thus double-modular redundant positioning sensors are introduced into the system. This paper studies switching algorithms for these redundant positioning sensors. At first, adaptive prediction is applied to the sensor signals. The prediction errors are used to trigger sensor switching. In order to enhance the reliability of the switching algorithm, wavelet analysis is introduced to suppress measuring disturbances without weakening the signal characteristics reflecting the stator joint gap based on the correlation between the wavelet coefficients of adjacent scales. The time delay characteristics of the method are analyzed to guide the algorithm simplification. Finally, the effectiveness of the simplified switching algorithm is verified through experiments. PMID:23112657

Switching LPV Control with Double-Layer LPV Model for Aero-Engines

NASA Astrophysics Data System (ADS)

Tang, Lili; Huang, Jinquan; Pan, Muxuan

2017-11-01

To cover the whole range of operating conditions of aero-engine, a double-layer LPV model is built so as to take into account of the variability due to the flight altitude, Mach number and the rotational speed. With this framework, the problem of designing LPV state-feedback robust controller that guarantees desired bounds on both H_∞ and H_2 performances is considered. Besides this, to reduce the conservativeness caused by a single LPV controller of the whole flight envelope and the common Lyapunov function method, a new method is proposed to design a family of LPV switching controllers. The switching LPV controllers can ensure that the closed-loop system remains stable in the sense of Lyapunov under arbitrary switching logic. Meanwhile, the switching LPV controllers can ensure the parameters change smoothly. The validity and performance of the theoretical results are demonstrated through a numerical example.

Silicon Carbide MOSFET-Based Switching Power Amplifier for Precision Magnet Control

NASA Astrophysics Data System (ADS)

Miller, Kenneth; Ziemba, Timothy; Prager, James; Picard, Julian

2016-10-01

Eagle Harbor Technologies, Inc. (EHT) is using the latest in solid-state switching technologies to advance the state-of-the-art in magnet control for fusion science. Silicon carbide (SiC) MOSFETs offer advantages over IGBTs including lower drive energy requirements, lower conduction and switching losses, and higher switching frequency capabilities. When comparing SiC and traditional silicon-based MOSFETs, SiC MOSFETs provide higher current carrying capability allowing for smaller package weights and sizes and lower operating temperature. To validate the design, EHT has developed a low-power switching power amplifier (SPA), which has been used for precision control of magnetic fields, including rapidly changing the fields in coils. This design has been incorporated in to a high power SPA, which has been bench tested. This high power SPA will be tested at the Helicity Injected Torus (HIT) at the University of Washington. Following successful testing, EHT will produce enough SiC MOSFET-based SPAs to replace all of the units at HIT, which allows for higher frequency operation and an overall increase in pulsed current levels.

Antisense Oligonucleotides Modulating Activation of a Nonsense-Mediated RNA Decay Switch Exon in the ATM Gene.

PubMed

Kralovicova, Jana; Moreno, Pedro M D; Cross, Nicholas C P; Pêgo, Ana Paula; Vorechovsky, Igor

2016-12-01

ATM (ataxia-telangiectasia, mutated) is an important cancer susceptibility gene that encodes a key apical kinase in the DNA damage response pathway. ATM mutations in the germ line result in ataxia-telangiectasia (A-T), a rare genetic syndrome associated with hypersensitivity to double-strand DNA breaks and predisposition to lymphoid malignancies. ATM expression is limited by a tightly regulated nonsense-mediated RNA decay (NMD) switch exon (termed NSE) located in intron 28. In this study, we identify antisense oligonucleotides that modulate NSE inclusion in mature transcripts by systematically targeting the entire 3.1-kb-long intron. Their identification was assisted by a segmental deletion analysis of transposed elements, revealing NSE repression upon removal of a distant antisense Alu and NSE activation upon elimination of a long terminal repeat transposon MER51A. Efficient NSE repression was achieved by delivering optimized splice-switching oligonucleotides to embryonic and lymphoblastoid cells using chitosan-based nanoparticles. Together, these results provide a basis for possible sequence-specific radiosensitization of cancer cells, highlight the power of intronic antisense oligonucleotides to modify gene expression, and demonstrate transposon-mediated regulation of NSEs.

Research on the influence of helical strakes on dynamic response of floating wind turbine platform

NASA Astrophysics Data System (ADS)

Ding, Qin-wei; Li, Chun

2017-04-01

The stability of platform structure is the paramount guarantee of the safe operation of the offshore floating wind turbine. The NREL 5MW floating wind turbine is established based on the OC3-Hywind Spar Buoy platform with the supplement of helical strakes for the purpose to analyze the impact of helical strakes on the dynamic response of the floating wind turbine Spar platform. The dynamic response of floating wind turbine Spar platform under wind, wave and current loading from the impact of number, height and pitch ratio of the helical strakes is analysed by the radiation and diffraction theory, the finite element method and orthogonal design method. The result reveals that the helical strakes can effectively inhibit the dynamic response of the platform but enlarge the wave exciting force; the best parameter combination is two pieces of helical strakes with the height of 15% D ( D is the diameter of the platform) and the pitch ratio of 5; the height of the helical strake and its pitch ratio have significant influence on pitch response.

Magnetic helices as metastable states of finite XY ferromagnetic chains: An analytical study

NASA Astrophysics Data System (ADS)

Popov, Alexander P.; Pini, Maria Gloria

2018-04-01

We investigated a simple but non trivial model, consisting of a chain of N classical XY spins with nearest neighbor ferromagnetic interaction, where each of the two end-point spins is assumed to be exchange-coupled to a fully-pinned fictitious spin. In the mean field approximation, the system might be representative of a soft ferromagnetic film sandwiched between two magnetically hard layers. We show that, while the ground state is ferromagnetic and collinear, the system can attain non-collinear metastable states in the form of magnetic helices. The helical solutions and their stability were studied analytically in the absence of an external magnetic field. There are four possible classes of solutions. Only one class is metastable, and its helical states contain an integer number of turns. Among the remaining unstable classes, there is a class of helices which contain an integer number of turns. Therefore, an integer number of turns in a helical configuration is a necessary, but not a sufficient, condition for metastability. These results may be useful to devise future applications of metastable magnetic helices as energy-storing elements.

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

Modeling of CMOS compatible ring resonator switch with intermediate vanadium oxide as the switching element

NASA Astrophysics Data System (ADS)

Singh, Mandeep; Datta, Arnab

2018-05-01

In this paper, silicon based dual ring resonator with hybrid plasmonic bus waveguides (Cu-SiO2-Si-SiO2-Cu) is investigated for achieving switching in the telecommunication C-band (λ = 1.54-1.553µm). The switch element uses vanadium oxide (VO2) as the switching medium when inserted between the rings in order to tailor transmission from one ring to the other through heating induced phase transition. In this manner, the proposed switch element uses one vanadium oxide medium instead of refractive index tailoring of the whole ring as in the prior reported works and achieves switching response. From two-dimensional finite element analysis we have found that, the proposed switch can achieve maximum extinction ratio of 2.72 dB at λ = 1.5434µm, exclusively by tailoring VO2 phase. Furthermore, impact of aperture width, and gap (separation between the bus waveguide and rings) are investigated to gain insight on the improvement of extinction ratio. From our numerical simulations, we find that free spectral range (FSR) and figure of merit (Q) for OFF and ON states are (173.36 nm, 92.63), and (173.58 nm, 65.39), respectively.

Rhenium(I)-based Double-heterostranded Helicates.

PubMed

Saxena, Priya; Shankar, Bhaskaran; Sathyanarayana, Arruri; Prabusankar, Ganesan; Sathiyendiran, Malaichamy

2015-01-01

Rhenium(I)-based supramolecular coordination complexes were obtained using Re2(CO)10, (2-hydroxyphenyl)benzimidazole-derived bis-chelating N∩O donors and a benzimidazolyl-derived ditopic monodentate N-donor possessing Troger's base spacer in a one-pot approach.

Charged-pion cross sections and double-helicity asymmetries in polarized p + p collisions at √s = 200 GeV

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

Adare, A.; Aidala, C.; Ajitanand, N. N.

2015-02-02

We present midrapidity charged-pion invariant cross sections, the ratio of the π⁻ to π⁺ cross sections and the charge-separated double-spin asymmetries in polarized p+p collisions at √s = 200 GeV. While the cross section measurements are consistent within the errors of next-to-leadingorder (NLO) perturbative quantum chromodynamics predictions (pQCD), the same calculations over estimate the ratio of the charged-pion cross sections. This discrepancy arises from the cancellation of the substantial systematic errors associated with the NLO-pQCD predictions in the ratio and highlights the constraints these data will place on flavor dependent pion fragmentation functions. Thus, the charge-separated pion asymmetries presented heremore » sample an x range of ~0.03–0.16 and provide unique information on the sign of the gluon-helicity distribution.« less

Enhanced Stability of DNA Nanostructures by Incorporation of Unnatural Base Pairs.

PubMed

Liu, Qing; Liu, Guocheng; Wang, Ting; Fu, Jing; Li, Rujiao; Song, Linlin; Wang, Zhen-Gang; Ding, Baoquan; Chen, Fei

2017-11-03

Self-assembled DNA nanostructures hold great promise in the fields of nanofabrication, biosensing and nanomedicine. However, the inherent low stability of the DNA double helices, formed by weak interactions, largely hinders the assembly and functions of DNA nanostructures. In this study, we redesigned and constructed a six-arm DNA junction by incorporation of the unnatural base pairs 5-Me-isoC/isoG and A/2-thioT into the double helices. They not only retained the structural integrity of the DNA nanostructure, but also showed enhanced thermal stability and resistance to T7 Exonuclease digestion. This research may expand the applications of DNA nanostructures in nanofabrication and biomedical fields, and furthermore, the genetic alphabet expansion with unnatural base pairs may enable us to construct more complicated and diversified self-assembled DNA nanostructures. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Charged-pion cross sections and double-helicity asymmetries in polarized p +p collisions at √{s }=200 GeV

NASA Astrophysics Data System (ADS)

Adare, A.; Aidala, C.; Ajitanand, N. N.; Akiba, Y.; Akimoto, R.; Al-Ta'Ani, H.; Alexander, J.; Andrews, K. R.; Angerami, A.; Aoki, K.; Apadula, N.; Appelt, E.; Aramaki, Y.; Armendariz, R.; Aschenauer, E. C.; Atomssa, E. T.; Awes, T. C.; Azmoun, B.; Babintsev, V.; Bai, M.; Bannier, B.; Barish, K. N.; Bassalleck, B.; Basye, A. T.; Bathe, S.; Baublis, V.; Baumann, C.; Bazilevsky, A.; Belmont, R.; Ben-Benjamin, J.; Bennett, R.; Blau, D. S.; Bok, J. S.; Boyle, K.; Brooks, M. L.; Broxmeyer, D.; Buesching, H.; Bumazhnov, V.; Bunce, G.; Butsyk, S.; Campbell, S.; Castera, P.; Chen, C.-H.; Chi, C. Y.; Chiu, M.; Choi, I. J.; Choi, J. B.; Choudhury, R. K.; Christiansen, P.; Chujo, T.; Chvala, O.; Cianciolo, V.; Citron, Z.; Cole, B. A.; Conesa Del Valle, Z.; Connors, M.; Csanád, M.; Csörgő, T.; Dairaku, S.; Datta, A.; David, G.; Dayananda, M. K.; Denisov, A.; Deshpande, A.; Desmond, E. J.; Dharmawardane, K. V.; Dietzsch, O.; Dion, A.; Donadelli, M.; Drapier, O.; Drees, A.; Drees, K. A.; Durham, J. M.; Durum, A.; D'Orazio, L.; Efremenko, Y. V.; Engelmore, T.; Enokizono, A.; En'yo, H.; Esumi, S.; Fadem, B.; Fields, D. E.; Finger, M.; Finger, M.; Fleuret, F.; Fokin, S. L.; Frantz, J. E.; Franz, A.; Frawley, A. D.; Fukao, Y.; Fusayasu, T.; Gal, C.; Garishvili, I.; Giordano, F.; Glenn, A.; Gong, X.; Gonin, M.; Goto, Y.; Granier de Cassagnac, R.; Grau, N.; Greene, S. V.; Grosse Perdekamp, M.; Gunji, T.; Guo, L.; Gustafsson, H.-Å.; Haggerty, J. S.; Hahn, K. I.; Hamagaki, H.; Hamblen, J.; Han, R.; Hanks, J.; Harper, C.; Hashimoto, K.; Haslum, E.; Hayano, R.; He, X.; Hemmick, T. K.; Hester, T.; Hill, J. C.; Hollis, R. S.; Holzmann, W.; Homma, K.; Hong, B.; Horaguchi, T.; Hori, Y.; Hornback, D.; Huang, S.; Ichihara, T.; Ichimiya, R.; Iinuma, H.; Ikeda, Y.; Imai, K.; Inaba, M.; Iordanova, A.; Isenhower, D.; Ishihara, M.; Issah, M.; Ivanischev, D.; Iwanaga, Y.; Jacak, B. V.; Jia, J.; Jiang, X.; John, D.; Johnson, B. M.; Jones, T.; Joo, K. S.; Jouan, D.; Kamin, J.; Kaneti, S.; Kang, B. H.; Kang, J. H.; Kang, J. S.; Kapustinsky, J.; Karatsu, K.; Kasai, M.; Kawall, D.; Kazantsev, A. V.; Kempel, T.; Khanzadeev, A.; Kijima, K. M.; Kim, B. I.; Kim, D. J.; Kim, E.-J.; Kim, Y.-J.; Kim, Y. K.; Kinney, E.; Kiss, Á.; Kistenev, E.; Kleinjan, D.; Kline, P.; Kochenda, L.; Komkov, B.; Konno, M.; Koster, J.; Kotov, D.; Král, A.; Kunde, G. J.; Kurita, K.; Kurosawa, M.; Kwon, Y.; Kyle, G. S.; Lacey, R.; Lai, Y. S.; Lajoie, J. G.; Lebedev, A.; Lee, D. M.; Lee, J.; Lee, K. B.; Lee, K. S.; Lee, S. H.; Lee, S. R.; Leitch, M. J.; Leite, M. A. L.; Li, X.; Lim, S. H.; Linden Levy, L. A.; Liu, H.; Liu, M. X.; Love, B.; Lynch, D.; Maguire, C. F.; Makdisi, Y. I.; Manion, A.; Manko, V. I.; Mannel, E.; Mao, Y.; Masui, H.; McCumber, M.; McGaughey, P. L.; McGlinchey, D.; McKinney, C.; Means, N.; Mendoza, M.; Meredith, B.; Miake, Y.; Mibe, T.; Mignerey, A. C.; Miki, K.; Milov, A.; Mitchell, J. T.; Miyachi, Y.; Mohanty, A. K.; Moon, H. J.; Morino, Y.; Morreale, A.; Morrison, D. P.; Motschwiller, S.; Moukhanova, T. V.; Murakami, T.; Murata, J.; Nagamiya, S.; Nagle, J. L.; Naglis, M.; Nagy, M. I.; Nakagawa, I.; Nakamiya, Y.; Nakamura, K. R.; Nakamura, T.; Nakano, K.; Newby, J.; Nguyen, M.; Nihashi, M.; Nouicer, R.; Nyanin, A. S.; Oakley, C.; O'Brien, E.; Ogilvie, C. A.; Oka, M.; Okada, K.; Oskarsson, A.; Ouchida, M.; Ozawa, K.; Pak, R.; Pantuev, V.; Papavassiliou, V.; Park, B. H.; Park, I. H.; Park, S. K.; Pate, S. F.; Patel, L.; Pei, H.; Peng, J.-C.; Pereira, H.; Peressounko, D. Yu.; Petti, R.; Pinkenburg, C.; Pisani, R. P.; Proissl, M.; Purschke, M. L.; Qu, H.; Rak, J.; Ravinovich, I.; Read, K. F.; Reygers, K.; Riabov, V.; Riabov, Y.; Richardson, E.; Roach, D.; Roche, G.; Rolnick, S. D.; Rosati, M.; Rosendahl, S. S. E.; Rubin, J. G.; Sahlmueller, B.; Saito, N.; Sakaguchi, T.; Samsonov, V.; Sano, S.; Sarsour, M.; Sato, T.; Savastio, M.; Sawada, S.; Sedgwick, K.; Seidl, R.; Seto, R.; Sharma, D.; Shein, I.; Shibata, T.-A.; Shigaki, K.; Shim, H. H.; Shimomura, M.; Shoji, K.; Shukla, P.; Sickles, A.; Silva, C. L.; Silvermyr, D.; Silvestre, C.; Sim, K. S.; Singh, B. K.; Singh, C. P.; Singh, V.; Slunečka, M.; Sodre, T.; Soltz, R. A.; Sondheim, W. E.; Sorensen, S. P.; Sourikova, I. V.; Stankus, P. W.; Stenlund, E.; Stoll, S. P.; Sugitate, T.; Sukhanov, A.; Sun, J.; Sziklai, J.; Takagui, E. M.; Takahara, A.; Taketani, A.; Tanabe, R.; Tanaka, Y.; Taneja, S.; Tanida, K.; Tannenbaum, M. J.; Tarafdar, S.; Taranenko, A.; Tennant, E.; Themann, H.; Thomas, D.; Togawa, M.; Tomášek, L.; Tomášek, M.; Torii, H.; Towell, R. S.; Tserruya, I.; Tsuchimoto, Y.; Utsunomiya, K.; Vale, C.; van Hecke, H. W.; Vazquez-Zambrano, E.; Veicht, A.; Velkovska, J.; Vértesi, R.; Virius, M.; Vossen, A.; Vrba, V.; Vznuzdaev, E.; Wang, X. R.; Watanabe, D.; Watanabe, K.; Watanabe, Y.; Watanabe, Y. S.; Wei, F.; Wei, R.; Wessels, J.; White, S. N.; Winter, D.; Woody, C. L.; Wright, R. M.; Wysocki, M.; Yamaguchi, Y. L.; Yang, R.; Yanovich, A.; Ying, J.; Yokkaichi, S.; Yoo, J. S.; You, Z.; Young, G. R.; Younus, I.; Yushmanov, I. E.; Zajc, W. A.; Zelenski, A.; Zhou, S.; Phenix Collaboration

2015-02-01

We present midrapidity charged-pion invariant cross sections, the ratio of the π- to π+ cross sections and the charge-separated double-spin asymmetries in polarized p +p collisions at √{s }=200 GeV . While the cross section measurements are consistent within the errors of next-to-leading-order (NLO) perturbative quantum chromodynamics predictions (pQCD), the same calculations overestimate the ratio of the charged-pion cross sections. This discrepancy arises from the cancellation of the substantial systematic errors associated with the NLO-pQCD predictions in the ratio and highlights the constraints these data will place on flavor-dependent pion fragmentation functions. The charge-separated pion asymmetries presented here sample an x range of ˜0.03 - 0.16 and provide unique information on the sign of the gluon-helicity distribution.

Helicity evolution at small x : Flavor singlet and nonsinglet observables

DOE PAGES

Kovchegov, Yuri V.; Pitonyak, Daniel; Sievert, Matthew D.

2017-01-30

We extend our earlier results for the quark helicity evolution at small x to derive the small-x asymptotics of the flavor singlet and flavor nonsinglet quark helicity TMDs and PDFs and of the g 1 structure function. In the flavor singlet case we rederive the evolution equations obtained in our previous paper on the subject, performing additional cross-checks of our results. In the flavor nonsinglet case we construct new small-x evolution equations by employing the large-N c limit. Here, all evolution equations resum double-logarithmic powers of α sln 2(1/x) in the polarization-dependent evolution along with the single-logarithmic powers of αmore » sln(1/x) in the unpolarized evolution which includes saturation effects.« less

Helicity evolution at small x : Flavor singlet and nonsinglet observables

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

Kovchegov, Yuri V.; Pitonyak, Daniel; Sievert, Matthew D.

We extend our earlier results for the quark helicity evolution at small x to derive the small-x asymptotics of the flavor singlet and flavor nonsinglet quark helicity TMDs and PDFs and of the g 1 structure function. In the flavor singlet case we rederive the evolution equations obtained in our previous paper on the subject, performing additional cross-checks of our results. In the flavor nonsinglet case we construct new small-x evolution equations by employing the large-N c limit. Here, all evolution equations resum double-logarithmic powers of α sln 2(1/x) in the polarization-dependent evolution along with the single-logarithmic powers of αmore » sln(1/x) in the unpolarized evolution which includes saturation effects.« less

Electrostatic contribution to twist rigidity of DNA.

PubMed

Mohammad-Rafiee, Farshid; Golestanian, Ramin

2004-06-01

The electrostatic contribution to the twist rigidity of DNA is studied, and it is shown that the Coulomb self-energy of the double-helical sugar-phosphate backbone makes a considerable contribution-the electrostatic twist rigidity of DNA is found to be C(elec) approximately 5 nm, which makes up about 7% of its total twist rigidity ( C(DNA) approximately 75 nm). The electrostatic twist rigidity is found, however, to depend only weakly on the salt concentration, because of a competition between two different screening mechanisms: (1) Debye screening by the salt ions in the bulk, and (2) structural screening by the periodic charge distribution along the backbone of the helical polyelectrolyte. It is found that, depending on the parameters, the electrostatic contribution to the twist rigidity could stabilize or destabilize the structure of a helical polyelectrolyte.

The spatial configuration of ordered polynucleotide chains. II. The poly(rA) helix.

PubMed Central

Olson, W K

1975-01-01

Approximate details of the spatial configuration of the ordered single-stranded poly(rA) molecule in dilute solution have been obtained in a combined theoretical analysis of base stacking and chain flexibility. Only those regularly repeating structures which fulfill the criterion of conformational flexibility (based upon all available experimental and theoretical evidence of preferred bond rotations) and which also exhibit the right-handed base stacking pattern observed in nmr investigations of poly(rA) are deemed suitable single-stranded helices. In addition, the helical geometry of the stacked structures is required to be consistent with the experimentally observed dimensions of both completely ordered and partially ordered poly(rA) chains. Only a single category of poly(rA) helices (very similar in all conformational details to the individual chains of the poly(rA) double-stranded X-ray structure) is thus obtained. Other conformationally feasible polynucleotide helices characterized simply by a parallel and overlapping base stacking arrangement are also discussed. PMID:1052529

Design and construction of a novel 1H/19F double-tuned coil system using PIN-diode switches at 9.4T.

PubMed

Choi, Chang-Hoon; Hong, Suk-Min; Ha, YongHyun; Shah, N Jon

2017-06-01

A double-tuned 1 H/ 19 F coil using PIN-diode switches was developed and its performance evaluated. The is a key difference from the previous developments being that this design used a PIN-diode switch in series with an additionally inserted inductor in parallel to one of the capacitors on the loop. The probe was adjusted to 19 F when the reverse bias voltage was applied (PIN-diode OFF), whilst it was switched to 1 H when forward current was flowing (PIN-diode ON). S-parameters and Q-factors of single- and double-tuned coils were examined and compared with/without a phantom on the bench. Imaging experiments were carried out on a 9.4T preclinical scanner. All coils were tuned at resonance frequencies and matched well. It is shown that the Q-ratio and SNR of double-tuned coil at 19 F frequency are nearly as good as those of a single-tuned coil. Since the operating frequency was tuned to 19 F when the PIN-diodes were turned off, losses due to PIN-diodes were substantially lower resulting in the provision of excellent image quality of X-nuclei. Copyright © 2017 Elsevier Inc. All rights reserved.

Design and Construction of Versatile Experiment Spherical Torus (VEST) at Seoul National University

NASA Astrophysics Data System (ADS)

An, Younghwa; Chung, Kyoung-Jae; Jung, Bongki; Lee, Hyunyeong; Sung, Choongki; Kim, Hyun-Seok; Na, Yong-Su; Hwang, Yong-Seok

2011-10-01

A new spherical torus, named as VEST (Versatile Experiment Spherical Torus), has been built at Seoul National University to investigate versatile research topics such as double null merging start-up, divertor engineering and non-inductive current drive. VEST is characterized by two partial solenoid coils installed at both vertical ends of a center stack, which will be used for double null merging start-up schemes. A poloidal field (PF) coil system including the partial solenoids for break-down and a long solenoid for the sustainment of merged plasma has been designed by solving circuit equations for the PF coils and vacuum vessel elements in consideration of required volt-second, null configuration and eddy current. To supply required currents to the PF coils and solenoids, power supplies based on double-swing circuit have been designed and fabricated with capacitor banks and thyristor switch assemblies. Also a power supply utilizing cost-effective commercial batteries has been developed for toroidal field(TF) coils. Detailed descriptions on the design of VEST and some initial test results will be presented.

A Josephson Junction based SPDT switch

NASA Astrophysics Data System (ADS)

Zhang, Helin; Earnest, Nathan; Lu, Yao; Ma, Ruichao; Chakram, Srivatsan; Schuster, David

RF microwave switches are useful tools in cryogenic experiments, allowing for multiple experiments to be connected to a single cryogenic measurement chain. However, these switches dissipate a substantial amount of heat, preventing fast switching. Josephson junction (JJ) are a promising avenue for realizing millikelvin microwave switching. We present a JJ based single-pole-double throw (SPDT) switch that has fast switching time, no heat dissipation, large on/off contrast, and works over a wide bandwidth. The switch can be used for real-time switching between experiments, routing single photons, or even generating entanglement. We will describe the design of the switch and present experimental characterization of its performance.

A yield-optimized access to double-helical SnIP via a Sn/SnI2 approach

NASA Astrophysics Data System (ADS)

Utrap, André; Xiang, Ng Yan; Nilges, Tom

2017-10-01

Herein we report on the optimized synthesis process of SnIP, the first inorganic double helix compound which shows high mechanical flexibility, a strong tendency for cleavage or delamination and intriguing electronic properties. In this work we analyzed the influence of SnI2 as a reaction promotor or mineralizer compound for the synthesis of SnIP. In previous studies Sn/SnI4 was used as a precursor and chemical transport agent for the SnIP synthesis but significant amounts of non-reacted tin halide (SnI2 and SnI4) remained after the formation of the target compound reducing its quality and yield. Significantly less tin halide residue can be observed which suggests a reduction of side-reactions. While the Sn/SnI4 couple works perfectly for the synthesis of the two-dimensional material phosphorene precursor black phosphorus the Sn/SnI2 couple is beneficial for the one-dimensional ternary polyphosphide SnIP. These results strongly encourage the theory of SnI2 as the important reaction intermediate in the synthesis of covalently-bonded polyphosphide substructures and element allotropes at elevated temperatures.

Improved Electro-Optical Switches

NASA Technical Reports Server (NTRS)

Nelson, Bruce N.; Cooper, Ronald F.

1994-01-01

Improved single-pole, double-throw electro-optical switches operate in switching times less than microsecond developed for applications as optical communication systems and networks of optical sensors. Contain no moving parts. In comparison with some prior electro-optical switches, these are simpler and operate with smaller optical losses. Beam of light switched from one output path to other by applying, to electro-optical crystal, voltage causing polarization of beam of light to change from vertical to horizontal.

Nonvolatile Ionic Two-Terminal Memory Device

NASA Technical Reports Server (NTRS)

Williams, Roger M.

1990-01-01

Conceptual solid-state memory device nonvolatile and erasable and has only two terminals. Proposed device based on two effects: thermal phase transition and reversible intercalation of ions. Transfer of sodium ions between source of ions and electrical switching element increases or decreases electrical conductance of element, turning switch "on" or "off". Used in digital computers and neural-network computers. In neural networks, many small, densely packed switches function as erasable, nonvolatile synaptic elements.

Amplitude-steered, pseudophased antenna array

NASA Technical Reports Server (NTRS)

Johnson, C. C.; Martel, R. J.; Dietrich, F. J.; Koloboff, G. J.

1975-01-01

Beam may be smoothly scanned around ring array without instantaneous phase transitions while maintaining constant radiated power by gradually transferring power from receding element to element next to leading edge of driven segment, and by accomplishing antenna element switching during intervals when no power is being applied to elements being switched.

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

Schellenberg, Matthew J; Appel, C Denise; Adhikari, Sanjay

The topoisomerase II (topo II) DNA incision-and-ligation cycle can be poisoned (for example following treatment with cancer chemotherapeutics) to generate cytotoxic DNA double-strand breaks (DSBs) with topo II covalently conjugated to DNA. Tyrosyl-DNA phosphodiesterase 2 (Tdp2) protects genomic integrity by reversing 5'-phosphotyrosyl–linked topo II–DNA adducts. Here, X-ray structures of mouse Tdp2–DNA complexes reveal that Tdp2 β–2-helix–β DNA damage–binding 'grasp', helical 'cap' and DNA lesion–binding elements fuse to form an elongated protein-DNA conjugate substrate-interaction groove. The Tdp2 DNA-binding surface is highly tailored for engagement of 5'-adducted single-stranded DNA ends and restricts nonspecific endonucleolytic or exonucleolytic processing. Structural, mutational and functional analysesmore » support a single–metal ion catalytic mechanism for the exonuclease-endonuclease-phosphatase (EEP) nuclease superfamily and establish a molecular framework for targeted small-molecule blockade of Tdp2-mediated resistance to anticancer topoisomerase drugs.« less

Conformational Flexibility Enables the Function of a BECN1 Region Essential for Starvation-Mediated Autophagy

DOE PAGES

Mei, Yang; Ramanathan, Arvind; Glover, Karen; ...

2016-03-03

BECN1 is essential for autophagy, a critical eukaryotic cellular homeostasis pathway. Here in this study, we delineate a highly conserved BECN1 domain located between previously characterized BH3 and coiled-coil domains and elucidate its structure and role in autophagy. The 2.0 Å sulfur-single-wavelength anomalous dispersion X-ray crystal structure of this domain demonstrates that its N-terminal half is unstructured while its C-terminal half is helical; hence, we name it the flexible helical domain (FHD). Circular dichroism spectroscopy, double electron–electron resonance–electron paramagnetic resonance, and small-angle X-ray scattering (SAXS) analyses confirm that the FHD is partially disordered, even in the context of adjacent BECN1more » domains. Molecular dynamic simulations fitted to SAXS data indicate that the FHD transiently samples more helical conformations. FHD helicity increases in 2,2,2-trifluoroethanol, suggesting it may become more helical upon binding. Finally, cellular studies show that conserved FHD residues are required for starvation-induced autophagy. Thus, the FHD likely undergoes a binding-associated disorder-to-helix transition, and conserved residues critical for this interaction are essential for starvation-induced autophagy.« less

Similarities and Differences between RNA and DNA Double-Helical Structures in Circular Dichroism Spectroscopy: A SAC-CI Study.

PubMed

Miyahara, Tomoo; Nakatsuji, Hiroshi; Sugiyama, Hiroshi

2016-11-17

The helical structures of DNA and RNA are investigated experimentally using circular dichroism (CD) spectroscopy. The signs and the shapes of the CD spectra are much different between the right- and left-handed structures as well as between DNA and RNA. The main difference lies in the sign at around 295 nm of the CD spectra: it is positive for the right-handed B-DNA and the left-handed Z-RNA but is negative for the left-handed Z-DNA and the right-handed A-RNA. We calculated the SAC-CI CD spectra of DNA and RNA using the tetramer models, which include both hydrogen-bonding and stacking interactions that are important in both DNA and RNA. The SAC-CI results reproduced the features at around 295 nm of the experimental CD spectra of each DNA and RNA, and elucidated that the strong stacking interaction between the two base pairs is the origin of the negative peaks at 295 nm of the CD spectra for both DNA and RNA. On the basis of these facts, we discuss the similarities and differences between RNA and DNA double-helical structures in the CD spectroscopy based on the ChiraSac methodology.

MicroRNAs form triplexes with double stranded DNA at sequence-specific binding sites; a eukaryotic mechanism via which microRNAs could directly alter gene expression

DOE PAGES

Paugh, Steven W.; Coss, David R.; Bao, Ju; ...

2016-02-04

MicroRNAs are important regulators of gene expression, acting primarily by binding to sequence-specific locations on already transcribed messenger RNAs (mRNA). Recent studies indicate that microRNAs may also play a role in up-regulating mRNA transcription levels, although a definitive mechanism has not been established. Double-helical DNA is capable of forming triple-helical structures through Hoogsteen and reverse Hoogsteen interactions in the major groove of the duplex, and we show physical evidence that microRNAs form triple-helical structures with duplex DNA, and identify microRNA sequences that favor triplex formation. We developed an algorithm (Trident) to search genome-wide for potential triplex-forming sites and show thatmore » several mammalian and non-mammalian genomes are enriched for strong microRNA triplex binding sites. We show that those genes containing sequences favoring microRNA triplex formation are markedly enriched (3.3 fold, p<2.2 x 10 -16) for genes whose expression is positively correlated with expression of microRNAs targeting triplex binding sequences. As a result, this work has thus revealed a new mechanism by which microRNAs can interact with gene promoter regions to modify gene transcription.« less

Molecular self-assembly in substituted alanine derivatives: XRD, Hirshfeld surfaces and DFT studies

NASA Astrophysics Data System (ADS)

Rajalakshmi, Periasamy; Srinivasan, Navaneethakrishnan; Sivaraman, Gandhi; Razak, Ibrahim Abdul; Rosli, Mohd Mustaqim; Krishnakumar, Rajaputi Venkatraman

2014-06-01

The molecular assemblage in the crystal structures of three modified chiral amino acids, two of which are isomeric D- and L-pairs boc-L-benzothienylalanine (BLA), boc-D-benzothienylalanine (BDA) and the other boc-D-naphthylalanine (NDA) differing from this pair very slightly in the chemical modification introduced, is accurately described. The aggregation of amino acid molecules is similar in all the crystals and may be described as a twisted double helical ladder in which two complementary long helical chains formed through O-H⋯O hydrogen bonds are interconnected through the characteristic head-to-tail N-H⋯O hydrogen bonds. Thus the molecular aggregation enabled through classical hydrogen bonds may be regarded as a mimic of the characteristic double helical structure of DNA. Also, precise structural information involving these amino acid molecules with lower symmetry exhibiting higher trigonal symmetry in their self-assembly is expected to throw light on the nature and strength of intermolecular interactions and their role in self-assembly of molecular aggregates, which are crucial in developing new or at least supplement existing crystal engineering strategies. Single crystal X-ray analysis and their electronic structures were calculated at the DFT level with a detailed analysis of Hirshfeld surfaces and fingerprint plots facilitating a comparison of intermolecular interactions in building different supramolecular architectures.

MicroRNAs form triplexes with double stranded DNA at sequence-specific binding sites; a eukaryotic mechanism via which microRNAs could directly alter gene expression

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

Paugh, Steven W.; Coss, David R.; Bao, Ju

MicroRNAs are important regulators of gene expression, acting primarily by binding to sequence-specific locations on already transcribed messenger RNAs (mRNA). Recent studies indicate that microRNAs may also play a role in up-regulating mRNA transcription levels, although a definitive mechanism has not been established. Double-helical DNA is capable of forming triple-helical structures through Hoogsteen and reverse Hoogsteen interactions in the major groove of the duplex, and we show physical evidence that microRNAs form triple-helical structures with duplex DNA, and identify microRNA sequences that favor triplex formation. We developed an algorithm (Trident) to search genome-wide for potential triplex-forming sites and show thatmore » several mammalian and non-mammalian genomes are enriched for strong microRNA triplex binding sites. We show that those genes containing sequences favoring microRNA triplex formation are markedly enriched (3.3 fold, p<2.2 x 10 -16) for genes whose expression is positively correlated with expression of microRNAs targeting triplex binding sequences. As a result, this work has thus revealed a new mechanism by which microRNAs can interact with gene promoter regions to modify gene transcription.« less

The Effect of Hierarchical Task Representations on Task Selection in Voluntary Task Switching

ERIC Educational Resources Information Center

Weaver, Starla M.; Arrington, Catherine M.

2013-01-01

The current study explored the potential for hierarchical representations to influence action selection during voluntary task switching. Participants switched between 4 individual task elements. In Experiment 1, participants were encouraged to represent the task elements as grouped within a hierarchy based on experimental manipulations of varying…

MEMS, Ka-Band Single-Pole Double-Throw (SPDT) Switch for Switched Line Phase Shifters

NASA Technical Reports Server (NTRS)

Scardelletti, Maximilian C.; Ponchak, George E.; Varaljay, Nicholas C.

2002-01-01

Ka-band MEMS doubly anchored cantilever beam capacitive shunt devices are used to demonstrate a MEMS SPDT switch fabricated on high resistivity silicon (HRS) utilizing finite ground coplanar waveguide (FGC) transmission lines. The SPDT switch has an insertion loss (IL), return loss (RL), and isolation of 0.3dB, 40dB, and 30 dB, respectively at Ka-band.

Scalable, high-capacity optical switches for Internet routers and moving platforms

NASA Astrophysics Data System (ADS)

Joe, In-Sung

Internet traffic nearly doubles every year, and we need faster routers with higher ports count, yet lower electrical power consumption. Current internet routers use electrical switches that consume large amounts of electrical power to operate at high data rates. These internet routers dissipate ˜ 10kW per rack, and their capacity is limited by cooling constraints. The power consumption is also critical for moving platforms. As avionics advance, the demand for larger capacity networks increases. Optical fibers are already chosen for high speed data transmission in advanced aircraft. In optical communication systems, integrated passive optical components, such as Array Waveguide Gratings (AWGs), have provided larger capacity with lower power consumption, because minimal electrical power is required for their operation. In addition, compact, wavelength-tunable semiconductor lasers with wide tuning ranges that can switch their wavelengths in tens of nanoseconds have been demonstrated. Here we present a wavelength-selective optical packet switch based on Waveguide Grating Routers (WGRs), passive splitters, and combiners. Tunable lasers on the transmitter side are the only active switching elements. The WGR is operated on multiple Free Spectral Ranges (FSRs) to achieve increased port count and switching capacity while maintaining strict-sense, non-blocking operation. Switching times of less than 24ns between two wavelengths covering three FSRs is demonstrated experimentally. The electrical power consumption, size, weight, and cost of our optical switch is compared with those of conventional electrical switches, showing substantial improvements at large throughputs (˜2 Tb/s full duplex). A revised switch design that does not suffer optical loss from star couplers is proposed. This switch design uses only WGRs, and it is suitable for networks with stringent power budgets. The burst nature of the optical packet transmission requires clock recovery for every incoming packet, and conventional continuous-mode receivers are not suitable for this application. An Embedded Clock Transport (ECT) technique is adopted here. The ECT combines a clock tone with the data payload before the transmission. Simple band pass filtering can extract the transmitted clock tone, and low pass filtering can recover the data. Error-free transmissions at 2.488 Gb/s with ˜16 ns clock recovery time were demonstrated.

Efficacy and safety of extended- versus immediate-release pramipexole in Japanese patients with advanced and L-dopa-undertreated Parkinson disease: a double-blind, randomized trial.

PubMed

Mizuno, Yoshikuni; Yamamoto, Mitsutoshi; Kuno, Sadako; Hasegawa, Kazuko; Hattori, Nobutaka; Kagimura, Tatsuro; Sarashina, Akiko; Rascol, Olivier; Schapira, Anthony H V; Barone, Paolo; Hauser, Robert A; Poewe, Werner

2012-01-01

To compare the efficacy, safety, tolerability, and trough plasma levels of pramipexole extended-release (ER) and pramipexole immediate-release (IR), and to assess the effects of overnight switching from an IR to an ER formulation, in L-dopa-treated patients with Parkinson disease (PD). After a 1- to 4-week screening/enrollment, 112 patients who had exhibited L-dopa-related problems or were receiving suboptimal L-dopa dosage were randomized in double-blind, double-dummy, 1:1 fashion to pramipexole ER once daily or pramipexole IR 2 to 3 times daily for 12 weeks, both titrated to a maximum daily dose of 4.5 mg. Successful completers of double-blind treatment were switched to open-label pramipexole ER, beginning with a 4-week dose-adjustment phase. Among the double-blind treatment patients (n = 56 in each group), Unified Parkinson's Disease Rating Scale Parts II+III total scores decreased significantly from baseline and to a similar degree with pramipexole ER and IR formulations. In each group, 47 double-blind patients (83.9%) reported adverse events (AEs), requiring withdrawal of 3 ER patients (5.4%) and 2 IR patients (3.6%). Trough plasma levels at steady state (at the same doses and dose-normalized concentrations) were also similar with both formulations. Among open-label treatment patients (n = 53 from IR to ER), 83% were successfully switched (no worsening of PD symptoms) to pramipexole ER. In L-dopa-treated patients, pramipexole ER and pramipexole IR demonstrated similar efficacy, safety, tolerability, and trough plasma levels. Patients can be safely switched overnight from pramipexole IR to pramipexole ER with no impact on efficacy.

Open and closed conformations of two SpoIIAA-like proteins (YP_749275.1 and YP_001095227.1) provide insights into membrane association and ligand binding

PubMed Central

Kumar, Abhinav; Lomize, Andrei; Jin, Kevin K.; Carlton, Dennis; Miller, Mitchell D.; Jaroszewski, Lukasz; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L.; Chiu, Hsiu-Ju; Clayton, Thomas; Das, Debanu; Deller, Marc C.; Duan, Lian; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Anna; Han, Gye Won; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Marciano, David; McMullan, Daniel; Morse, Andrew T.; Nigoghossian, Edward; Okach, Linda; Reyes, Ron; Rife, Christopher L.; Sefcovic, Natasha; Tien, Henry J.; Trame, Christine B.; van den Bedem, Henry; Weekes, Dana; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

2010-01-01

The crystal structures of the proteins encoded by the YP_749275.1 and YP_001095227.1 genes from Shewanella frigidimarina and S. loihica, respectively, have been determined at 1.8 and 2.25 Å resolution, respectively. These proteins are members of a novel family of bacterial proteins that adopt the α/β SpoIIAA-like fold found in STAS and CRAL-TRIO domains. Despite sharing 54% sequence identity, these two proteins adopt distinct conformations arising from different dispositions of their α2 and α3 helices. In the ‘open’ conformation (YP_001095227.1), these helices are 15 Å apart, leading to the creation of a deep nonpolar cavity. In the ‘closed’ structure (YP_749275.1), the helices partially unfold and rearrange, occluding the cavity and decreasing the solvent-exposed hydrophobic surface. These two complementary structures are reminiscent of the conformational switch in CRAL-TRIO carriers of hydrophobic compounds. It is suggested that both proteins may associate with the lipid bilayer in their ‘open’ monomeric state by inserting their amphiphilic helices, α2 and α3, into the lipid bilayer. These bacterial proteins may function as carriers of nonpolar substances or as interfacially activated enzymes. PMID:20944218

Design of the Helicity Injected Torus with Steady Inductive Helicity Injection (HIT-SI)

NASA Astrophysics Data System (ADS)

Sieck, P. E.; Gu, P.; Hamp, W. T.; Izzo, V. A.; McCollam, K. J.; Jarboe, T. R.; Nelson, B. A.; Redd, A. J.; Rogers, J. A.; Shumlak, U.

2000-10-01

Steady Inductive Helicity Injection (SIHI) is an inductive current drive method that injects helicity at a nearly constant rate, without open field lines, and without removing any helicity or magnetic energy from the plasma(T.R. Jarboe, Fusion Technology 36), p. 85, 1999. SIHI directly produces a rotating magnetic field structure, and the current profile is nearly time independent in the frame of the rotating field. The Helicity Injected Torus with SIHI (HIT-SI) is a ``bow tie'' spheromak designed to implement SIHI so that the current profile in the rotating frame is optimized. SIHI is accomplished using two inductive helicity injectors that operate 90^o out of phase with each other. Each helicity injector is a 180^o segment of a ZT-P size (a ≈ 8cm, R ≈ 32cm) RFP. The presence of a spheromak equilibrium will be readily apparent on several diagnostics, including the surface magnetic probes. The design of HIT-SI is presented, including the manufacturing techniques and metallurgical processes being used in the construction of the one-meter diameter close-fitting flux conserver. Several small prototype tests have been performed to prove the vacuum seal and electrical insulation capabilities of the design, and a finite element stress analysis of the flux conserver will be presented.

Hybrid power source

DOEpatents

Singh, Harmohan N.

2012-06-05

A hybrid power system is comprised of a high energy density element such as a fuel-cell and high power density elements such as a supercapacitor banks. A DC/DC converter electrically connected to the fuel cell and converting the energy level of the energy supplied by the fuel cell. A first switch is electrically connected to the DC/DC converter. First and second supercapacitors are electrically connected to the first switch and a second switch. A controller is connected to the first switch and the second switch, monitoring charge levels of the supercapacitors and controls the switching in response to the charge levels. A load is electrically connected to the second switch. The first switch connects the DC/DC converter to the first supercapacitor when the second switch connects the second supercapacitor to the load. The first switch connects the DC/DC converter to the second supercapacitor when the second switch connects the first supercapacitor to the load.

Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics

PubMed Central

Liberman, Joseph A.; Suddala, Krishna C.; Aytenfisu, Asaminew; Chan, Dalen; Belashov, Ivan A.; Salim, Mohammad; Mathews, David H.; Spitale, Robert C.; Walter, Nils G.; Wedekind, Joseph E.

2015-01-01

PreQ1-III riboswitches are newly identified RNA elements that control bacterial genes in response to preQ1 (7-aminomethyl-7-deazaguanine), a precursor to the essential hypermodified tRNA base queuosine. Although numerous riboswitches fold as H-type or HLout-type pseudoknots that integrate ligand-binding and regulatory sequences within a single folded domain, the preQ1-III riboswitch aptamer forms a HLout-type pseudoknot that does not appear to incorporate its ribosome-binding site (RBS). To understand how this unusual organization confers function, we determined the crystal structure of the class III preQ1 riboswitch from Faecalibacterium prausnitzii at 2.75 Å resolution. PreQ1 binds tightly (KD,app 6.5 ± 0.5 nM) between helices P1 and P2 of a three-way helical junction wherein the third helix, P4, projects orthogonally from the ligand-binding pocket, exposing its stem-loop to base pair with the 3′ RBS. Biochemical analysis, computational modeling, and single-molecule FRET imaging demonstrated that preQ1 enhances P4 reorientation toward P1–P2, promoting a partially nested, H-type pseudoknot in which the RBS undergoes rapid docking (kdock ∼0.6 s−1) and undocking (kundock ∼1.1 s−1). Discovery of such dynamic conformational switching provides insight into how a riboswitch with bipartite architecture uses dynamics to modulate expression platform accessibility, thus expanding the known repertoire of gene control strategies used by regulatory RNAs. PMID:26106162

Computation of parton distributions from the quasi-PDF approach at the physical point

NASA Astrophysics Data System (ADS)

Alexandrou, Constantia; Bacchio, Simone; Cichy, Krzysztof; Constantinou, Martha; Hadjiyiannakou, Kyriakos; Jansen, Karl; Koutsou, Giannis; Scapellato, Aurora; Steffens, Fernanda

2018-03-01

We show the first results for parton distribution functions within the proton at the physical pion mass, employing the method of quasi-distributions. In particular, we present the matrix elements for the iso-vector combination of the unpolarized, helicity and transversity quasi-distributions, obtained with Nf = 2 twisted mass cloverimproved fermions and a proton boosted with momentum |p→| = 0.83 GeV. The momentum smearing technique has been applied to improve the overlap with the proton boosted state. Moreover, we present the renormalized helicity matrix elements in the RI' scheme, following the non-perturbative renormalization prescription recently developed by our group.

Small differences in amylopectin fine structure may explain large functional differences of starch.

PubMed

Bertoft, Eric; Annor, George A; Shen, Xinyu; Rumpagaporn, Pinthip; Seetharaman, Koushik; Hamaker, Bruce R

2016-04-20

Four amylose-free waxy rice starches were found to give rise to gels with clearly different morphology after storage for seven days at 4°C. The thermal and rheological properties of these gels were also different. This was remarkable in light of the subtle differences in the molecular structure of the amylopectin in the samples. Addition of iodine to the amylopectin samples suggested that not only external chains, but also the internal chains of amylopectin, could form helical inclusion complexes. It is suggested that these internal helical segments participate in the retrogradation of amylopectin, thereby stabilising the gels through double helical structures with external chains of adjacent molecules. Albeit few in number, such interactions appear to have important influences on starch functional properties. Copyright © 2015 Elsevier Ltd. All rights reserved.

Static magnetism and thermal switching in randomly oriented L10 FePt thin films

NASA Astrophysics Data System (ADS)

Lisfi, A.; Pokharel, S.; Alqarni, A.; Akioya, O.; Morgan, W.; Wuttig, M.

2018-05-01

Static magnetism and thermally activated magnetic relaxation were investigated in granular FePt films (20 nm-200 nm thick) with random magnetic anisotropy through hysteresis loop, torque curve and magnetization time dependence measurements. While the magnetism of thicker film (200 nm thick) is dominated by a single switching of the ordered L10 phase, thinner film (20 nm) displays a double switching, which is indicative of the presence of the disordered cubic phase. The pronounced behavior of double switching in thinner film suggests that the film grain boundary is composed of soft cubic magnetic phase. The magnetic relaxation study reveals that magnetic viscosity S of the films is strongly dependent on the external applied field and exhibits a maximum value (12 kAm) around the switching field and a vanishing behavior at low (1 kOe) and large (12 kOe) fields. The activation volume of the thermal switching was found to be much smaller than the physical volume of the granular structure due to the incoherent rotation mode of the magnetization reversal mechanism, which is established to be domain wall nucleation.

Gear Design Effects on the Performance of High Speed Helical Gear Trains as Used in Aerospace Drive Systems

NASA Technical Reports Server (NTRS)

Handschuh, R.; Kilmain, D.; Ehinger, R.; Sinusas, E.

2013-01-01

The performance of high-speed helical gear trains is of particular importance for tiltrotor aircraft drive systems. These drive systems are used to provide speed reduction/torque multiplication from the gas turbine output shaft and provide the necessary offset between these parallel shafts in the aircraft. Four different design configurations have been tested in the NASA Glenn Research Center, High Speed Helical Gear Train Test Facility. The design configurations included the current aircraft design, current design with isotropic superfinished gear surfaces, double helical design (inward and outward pumping), increased pitch (finer teeth), and an increased helix angle. All designs were tested at multiple input shaft speeds (up to 15,000 rpm) and applied power (up to 5,000 hp). Also two lubrication, system-related, variables were tested: oil inlet temperature (160 to 250 F) and lubricating jet pressure (60 to 80 psig). Experimental data recorded from these tests included power loss of the helical system under study, the temperature increase of the lubricant from inlet to outlet of the drive system and fling off temperatures (radially and axially). Also, all gear systems were tested with and without shrouds around the gears. The empirical data resulting from this study will be useful to the design of future helical gear train systems anticipated for next generation rotorcraft drive systems.

Gear Design Effects on the Performance of High Speed Helical Gear Trains as Used in Aerospace Drive Systems

NASA Technical Reports Server (NTRS)

Handschuh, R.; Kilmain, C.; Ehinger, R.; Sinusas, E.

2013-01-01

The performance of high-speed helical gear trains is of particular importance for tiltrotor aircraft drive systems. These drive systems are used to provide speed reduction / torque multiplication from the gas turbine output shaft and provide the necessary offset between these parallel shafts in the aircraft. Four different design configurations have been tested in the NASA Glenn Research Center, High Speed Helical Gear Train Test Facility. The design configurations included the current aircraft design, current design with isotropic superfinished gear surfaces, double helical design (inward and outward pumping), increased pitch (finer teeth), and an increased helix angle. All designs were tested at multiple input shaft speeds (up to 15,000 rpm) and applied power (up to 5,000 hp). Also two lubrication, system-related, variables were tested: oil inlet temperature (160 to 250 degF) and lubricating jet pressure (60 to 80 psig). Experimental data recorded from these tests included power loss of the helical system under study, the temperature increase of the lubricant from inlet to outlet of the drive system and fling off temperatures (radially and axially). Also, all gear systems were tested with and without shrouds around the gears. The empirical data resulting from this study will be useful to the design of future helical gear train systems anticipated for next generation rotorcraft drive systems.

Interconnecting network for switching data packets and method for switching data packets

DOEpatents

Benner, Alan Frederic; Minkenberg, Cyriel Johan Agnes; Stunkel, Craig Brian

2010-05-25

The interconnecting network for switching data packets, having data and flow control information, comprises a local packet switch element (S1) with local input buffers (I(1,1) . . . I(1,y)) for buffering the incoming data packets, a remote packet switch element (S2) with remote input buffers (I(2,1) . . . I(2,y)) for buffering the incoming data packets, and data lines (L) for interconnecting the local and the remote packet switch elements (S1, S2). The interconnecting network further comprises a local and a remote arbiter (A1, A2) which are connected via control lines (CL) to the input buffers (I(1,1) . . . I(1,y), I(2,1) . . . I(2,y)), and which are formed such that they can provide that the flow control information is transmitted via the data lines (L) and the control lines (CL).

Shifting the equilibrium mixture of gramicidin double helices toward a single conformation with multivalent cationic salts.

PubMed Central

Doyle, D A; Wallace, B A

1998-01-01

The conformation of the polypeptide antibiotic gramicidin is greatly influenced by its environment. In methanol, it exists as an equilibrium mixture of four interwound double-helical conformers that differ in their handedness, chain orientation, and alignment. Upon the addition of multivalent cationic salts, there is a shift in the equilibrium to a single conformer, which was monitored in this study by circular dichroism spectroscopy. With increasing concentrations of multivalent cations, both the magnitude of the entire spectrum and the ratio of the 229-nm to the 210-nm peak were increased. The spectral change is not related to the charge on the cation, but appears to be related to the cationic radius, with the maximum change in ellipticity occurring for cations with a radius of approximately 1 A. The effect requires the presence of an anion whose radius is greater than that of a fluoride ion, but is otherwise not a function of anion type. It is postulated that multivalent cations interact with a binding site in one of the conformers, known as species 1 (a left-handed, parallel, no stagger double helix), stabilizing a modified form of this type of structure. PMID:9675165

Double quick, double click reversible peptide "stapling".

PubMed

Grison, Claire M; Burslem, George M; Miles, Jennifer A; Pilsl, Ludwig K A; Yeo, David J; Imani, Zeynab; Warriner, Stuart L; Webb, Michael E; Wilson, Andrew J

2017-07-01

The development of constrained peptides for inhibition of protein-protein interactions is an emerging strategy in chemical biology and drug discovery. This manuscript introduces a versatile, rapid and reversible approach to constrain peptides in a bioactive helical conformation using BID and RNase S peptides as models. Dibromomaleimide is used to constrain BID and RNase S peptide sequence variants bearing cysteine (Cys) or homocysteine ( h Cys) amino acids spaced at i and i + 4 positions by double substitution. The constraint can be readily removed by displacement of the maleimide using excess thiol. This new constraining methodology results in enhanced α-helical conformation (BID and RNase S peptide) as demonstrated by circular dichroism and molecular dynamics simulations, resistance to proteolysis (BID) as demonstrated by trypsin proteolysis experiments and retained or enhanced potency of inhibition for Bcl-2 family protein-protein interactions (BID), or greater capability to restore the hydrolytic activity of the RNAse S protein (RNase S peptide). Finally, use of a dibromomaleimide functionalized with an alkyne permits further divergent functionalization through alkyne-azide cycloaddition chemistry on the constrained peptide with fluorescein, oligoethylene glycol or biotin groups to facilitate biophysical and cellular analyses. Hence this methodology may extend the scope and accessibility of peptide stapling.

Objective Molecular Dynamics with Self-consistent Charge Density Functional Tight-Binding (SCC-DFTB) Method

NASA Astrophysics Data System (ADS)

Dumitrica, Traian; Hourahine, Ben; Aradi, Balint; Frauenheim, Thomas

We discus the coupling of the objective boundary conditions into the SCC density functional-based tight binding code DFTB+. The implementation is enabled by a generalization to the helical case of the classical Ewald method, specifically by Ewald-like formulas that do not rely on a unit cell with translational symmetry. The robustness of the method in addressing complex hetero-nuclear nano- and bio-fibrous systems is demonstrated with illustrative simulations on a helical boron nitride nanotube, a screw dislocated zinc oxide nanowire, and an ideal double-strand DNA. Work supported by NSF CMMI 1332228.

Interplay of valley selection and helicity exchange of light in Raman scattering for graphene and MoS2

NASA Astrophysics Data System (ADS)

Tatsumi, Yuki; Saito, Riichiro

2018-03-01

Raman spectra of graphene and MoS2 are calculated for incident and scattered circularly polarized light. In the case of graphene, the well known G -band Raman spectra have a not well known property that the helicity of the incident circularly polarized light changes to another helicity in the scattered light. Using the electron-photon and electron-phonon matrix elements by first-principles calculation, we calculate resonant Raman spectra of graphene and MoS2 for circularly polarized light which are compared with recent experiments. The Raman intensity for circularly polarized light is relevant to optical valley polarization in the case of MoS2. We also discuss how the helicity-selection rule can be modified by applying stress to graphene.

Fin-line PIN-diode attenuators and switches for 94 GHz range

NASA Astrophysics Data System (ADS)

Meinel, H.; Callsen, H.

1982-06-01

The letter reports new results of fin-line PIN-diode attenuators and switches for the 94 GHz range. Design and performance of SPST and SPDT switches - single pole single throw and single pole double throw, respectively - will be presented. The attenuation of the SPST switch, for example, can be adjusted between 2 and 35 dB over the entire waveguide band from 75 to 110 GHz.

A switch from parallel to antiparallel strand orientation in a coiled-coil X-ray structure via two core hydrophobic mutations

DOE PAGES

Malashkevich, Vladimir N.; Higgins, Chelsea D.; Almo, Steven C.; ...

2015-05-06

The coiled-coil is one of the most ubiquitous and well studied protein structural motifs. Significant effort has been devoted to dissecting subtle variations of the typical heptad repeat sequence pattern that can designate larger topological features such as relative α-helical orientation and oligomer size. Here in this paper we report the X-ray structure of a model coiled-coil peptide, HA2-Del-L2seM, which forms an unanticipated core antiparallel dimer with potential sites for discrete higher-order multimerization (trimer or tetramer). In the X-ray structure, a third, partially-ordered α-helix is weakly associated with the antiparallel dimer and analytical ultracentrifugation experiments indicate the peptide forms amore » well-defined tetramer in solution. The HA2-Del-L2seM sequence is closely related to a parent model peptide, HA2-Del, which we previously reported adopts a parallel trimer; HA2-Del-L2seM differs by only hydrophobic leucine to selenomethione mutations and thus this subtle difference is sufficient to switch both relative α-helical topology and number of α-helices participating in the coiled-coil. Comparison of the X-ray structures of HA2-Del-L2seM (reported here) with the HA2-Del parent (reported previously) reveals novel interactions involving the selenomethionine residues that promote antiparallel coiled-coil configuration and preclude parallel trimer formation. Finally, these novel atomic insights are instructive for understanding subtle features that can affect coiled-coil topology and provide additional information for design of antiparallel coiled-coils.« less

Submolecular Structure and Orientation of Oligonucleotide Duplexes Tethered to Gold Electrodes Probed by Infrared Reflection Absorption Spectroscopy: Effect of the Electrode Potentials.

PubMed

Kékedy-Nagy, László; Ferapontova, Elena E; Brand, Izabella

2017-02-23

Unique electronic and ligand recognition properties of the DNA double helix provide basis for DNA applications in biomolecular electronic and biosensor devices. However, the relation between the structure of DNA at electrified interfaces and its electronic properties is still not well understood. Here, potential-driven changes in the submolecular structure of DNA double helices composed of either adenine-thymine (dAdT) 25 or cytosine-guanine (dGdC) 20 base pairs tethered to the gold electrodes are for the first time analyzed by in situ polarization modulation infrared reflection absorption spectroscopy (PM IRRAS) performed under the electrochemical control. It is shown that the conformation of the DNA duplexes tethered to gold electrodes via the C 6 alkanethiol linker strongly depends on the nucleic acid sequence composition. The tilt of purine and pyrimidine rings of the complementary base pairs (dAdT and dGdC) depends on the potential applied to the electrode. By contrast, neither the conformation nor orientation of the ionic in character phosphate-sugar backbone is affected by the electrode potentials. At potentials more positive than the potential of zero charge (pzc), a gradual tilting of the double helix is observed. In this tilted orientation, the planes of the complementary purine and pyrimidine rings lie ideally parallel to each other. These potentials do not affect the integral stability of the DNA double helix at the charged interface. At potentials more negative than the pzc, DNA helices adopt a vertical to the gold surface orientation. Tilt of the purine and pyrimidine rings depends on the composition of the double helix. In monolayers composed of (dAdT) 25 molecules the rings of the complementary base pairs lie parallel to each other. By contrast, the tilt of purine and pyrimidine rings in (dGdC) 20 helices depends on the potential applied to the electrode. Such potential-induced mobility of the complementary base pairs can destabilize the helix structure at a submolecular level. These pioneer results on the potential-driven changes in the submolecular structure of double stranded DNA adsorbed on conductive supports contribute to further understanding of the potential-driven sequence-specific electronic properties of surface-tethered oligonucleotides.

SPARK GAP SWITCH

DOEpatents

Neal, R.B.

1957-12-17

An improved triggered spark gap switch is described, capable of precisely controllable firing time while switching very large amounts of power. The invention in general comprises three electrodes adjustably spaced and adapted to have a large potential impressed between the outer electrodes. The central electrode includes two separate elements electrically connected togetaer and spaced apart to define a pair of spark gaps between the end electrodes. Means are provided to cause the gas flow in the switch to pass towards the central electrode, through a passage in each separate element, and out an exit disposed between the two separate central electrode elements in order to withdraw ions from the spark gap.

A Hybrid Converter for Improving Light Load Efficiency

NASA Astrophysics Data System (ADS)

Takahashi, Masaya; Nishijima, Kimihiro; Nagao, Michihiko; Sato, Terukazu; Nabeshima, Takashi

In order to reduce power consumption of electronic equipment in stand-by mode, idle-mode and sleep-mode, a simple efficiency improvement technique for switching regulator in light load region is proposed. In this technique, under the light load, the small switching elements in a MOSFET driver circuit are used instead of the switching elements in a main regulator circuit to reduce driving losses. Of course, under the load heavier than light load, the MOSFET driver drives the switching elements in the main regulator circuit. The efficiency of a 2.5V/5A prototype buck converter is improved from 47.1% to 72.7% by using the proposed technique.

Role of Al2O3 thin layer on improving the resistive switching properties of Ta5Si3-based conductive bridge random accesses memory device

NASA Astrophysics Data System (ADS)

Kumar, Dayanand; Aluguri, Rakesh; Chand, Umesh; Tseng, Tseung-Yuen

2018-04-01

Ta5Si3-based conductive bridge random access memory (CBRAM) devices have been investigated to improve their resistive switching characteristics for their application in future nonvolatile memory technology. Changes in the switching characteristics by the addition of a thin Al2O3 layer of different thicknesses at the bottom electrode interface of a Ta5Si3-based CBRAM devices have been studied. The double-layer device with a 1 nm Al2O3 layer has shown improved resistive switching characteristics over the single layer one with a high on/off resistance ratio of 102, high endurance of more than 104 cycles, and good retention for more than 105 s at the temperature of 130 °C. The higher thermal conductivity of Al2O3 over Ta5Si3 has been attributed to the enhanced switching properties of the double-layer devices.

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

Nuclear breeder reactor fuel element with silicon carbide getter

DOEpatents

Christiansen, David W.; Karnesky, Richard A.

1987-01-01

An improved cesium getter 28 is provided in a breeder reactor fuel element or pin in the form of an extended surface area, low density element formed in one embodiment as a helically wound foil 30 located with silicon carbide, and located at the upper end of the fertile material upper blanket 20.

Biomechanical comparison of straight and helical compression plates for fixation of transverse and oblique bone fractures: Modeling and experiments.

PubMed

Sezek, Sinan; Aksakal, Bunyamin; Gürger, Murat; Malkoc, Melih; Say, Y

2016-08-12

Total deformation and stability of straight and helical compression plates were studied by means of the finite element method (FEM) and in vitro biomechanical experiments. Fixations of transverse (TF) and oblique (45°) bone (OF) fractures have been analyzed on sheep tibias by designing the straight compression (SP) and Helical Compression Plate (HP) models. The effects of axial compression, bending and torsion loads on both plating systems were analyzed in terms of total displacements. Numerical models and experimental models suggested that under compression loadings, bone fracture gap closures for both fracture types were found to be in the favor of helical plate designs. The helical plate (HP) fixations provided maximum torsional resistance compared to the (SP) fixations. The fracture gap closure and stability of helical plate fixation for transverse fractures was determined to be higher than that found for the oblique fractures. The comparison of average compression stress, bending and torsion moments showed that the FEM and experimental results are in good agreement and such designs are likely to have a positive impact in future bone fracture fixation designs.

High-speed on-chip windowed centroiding using photodiode-based CMOS imager

NASA Technical Reports Server (NTRS)

Pain, Bedabrata (Inventor); Sun, Chao (Inventor); Yang, Guang (Inventor); Cunningham, Thomas J. (Inventor); Hancock, Bruce (Inventor)

2003-01-01

A centroid computation system is disclosed. The system has an imager array, a switching network, computation elements, and a divider circuit. The imager array has columns and rows of pixels. The switching network is adapted to receive pixel signals from the image array. The plurality of computation elements operates to compute inner products for at least x and y centroids. The plurality of computation elements has only passive elements to provide inner products of pixel signals the switching network. The divider circuit is adapted to receive the inner products and compute the x and y centroids.

High-speed on-chip windowed centroiding using photodiode-based CMOS imager

NASA Technical Reports Server (NTRS)

Pain, Bedabrata (Inventor); Sun, Chao (Inventor); Yang, Guang (Inventor); Cunningham, Thomas J. (Inventor); Hancock, Bruce (Inventor)

2004-01-01

A centroid computation system is disclosed. The system has an imager array, a switching network, computation elements, and a divider circuit. The imager array has columns and rows of pixels. The switching network is adapted to receive pixel signals from the image array. The plurality of computation elements operates to compute inner products for at least x and y centroids. The plurality of computation elements has only passive elements to provide inner products of pixel signals the switching network. The divider circuit is adapted to receive the inner products and compute the x and y centroids.

Chiral direction and interconnection of helical three-connected networks in metal-organic frameworks.

PubMed

Prior, T J; Rosseinsky, M J

2003-03-10

The control of the interpenetration and chirality of a family of metal-organic frameworks is discussed. These systems contain two- (A) and four-fold (B) interpenetration of helical three-connected networks generated by binding the 1,3,5-benzenetricarboxylate (btc) ligand to a metal center. These frameworks have the general formula Ni(3)(btc)(2)X(m)Y(n).solvent (where X = pyridine or 4-picoline, Y = ethylene glycol, 1,2-propanediol, 1,4-butanediol, meso-2,3-butanediol, 1,2,6-hexanetriol, glycerol). The structural and chemical effects of modifying the alcohol and aromatic amine ligands bound to the metal center include controlling the thermal stability and the degree of interpenetration. Covalent linking of the four interpenetrating networks in the A family and the switching of diol binding from mono- to bidentate are demonstrated. Recognition of chiral diols by the hand of the network helices is investigated by binding an alcohol ligand with two chiral centers of opposite sense to the same helix. This reveals the subtle nature of the helix-ligand interaction.

Helical unwinding and side-chain unlocking unravel the outward open conformation of the melibiose transporter

NASA Astrophysics Data System (ADS)

Wang, Li-Ying; Ravi, Vidhya M.; Leblanc, Gérard; Padrós, Esteve; Cladera, Josep; Perálvarez-Marín, Alex

2016-09-01

Molecular dynamics simulations have been used to study the alternate access mechanism of the melibiose transporter from Escherichia coli. Starting from the outward-facing partially occluded form, 2 out of 12 simulations produced an outward full open form and one partially open, whereas the rest yielded fully or partially occluded forms. The shape of the outward-open form resembles other outward-open conformations of secondary transporters. During the transporter opening, conformational changes in some loops are followed by changes in the periplasm region of transmembrane helix 7. Helical curvature relaxation and unlocking of hydrophobic and ionic locks promote the outward opening of the transporter making accessible the substrate binding site. In particular, FRET studies on mutants of conserved aromatic residues of extracellular loop 4 showed lack of substrate binding, emphasizing the importance of this loop for making crucial interactions that control the opening of the periplasmic side. This study indicates that the alternate access mechanism for the melibiose transporter fits better into a flexible gating mechanism rather than the archetypical helical rigid-body rocker-switch mechanism.

Switch Using Radio Frequency Identification

NASA Technical Reports Server (NTRS)

Fink, Patrick W. (Inventor); Kennedy, Timothy F. (Inventor); Lin, Gregory Y. (Inventor); Ngo, Phong H. (Inventor)

2015-01-01

Disclosed is an apparatus for use as a switch. In one embodiment, the switch comprises at least one RFID tag, each RFID tag comprising an antenna element and an RFID integrated circuit, at least one source element, and at least one lever arm. Each lever arm is connected to one of the RFID tags, and each lever arm is capable of two positions. One of the positions places the lever arm and the RFID tag connected thereto into alignment with the source element. Other embodiments are also described.

ADP/ATP mitochondrial carrier MD simulations to shed light on the structural-dynamical events that, after an additional mutation, restore the function in a pathological single mutant.

PubMed

Di Marino, Daniele; Oteri, Francesco; Morozzo Della Rocca, Blasco; Chillemi, Giovanni; Falconi, Mattia

2010-12-01

Molecular dynamics simulations of the wild type bovine ADP/ATP mitochondrial carrier, and of the single Ala113Pro and double Ala113Pro/Val180Met mutants, embedded in a lipid bilayer, have been carried out for 30ns to shed light on the structural-dynamical changes induced by the Val180Met mutation restoring the carrier function in the Ala113Pro pathologic mutant. Principal component analysis indicates that, for the three systems, the protein dynamics is mainly characterized by the motion of the matrix loops and of the odd-numbered helices having a conserved proline in their central region. Analysis of the motions shows a different behaviour of single pathological mutant with respect of the other two systems. The single mutation induces a regularization and rigidity of the H3 helix, lost upon the introduction of the second mutation. This is directly correlated to the salt bridge distribution involving residues Arg79, Asp134 and Arg234, hypothesized to interact with the substrate. In fact, in the wild type simulation two stable inter-helices salt bridges, crucial for substrate binding, are present almost over all the simulation time. In line with the impaired ADP transport, one salt interaction is lost in the single mutant trajectory but reappears in the double mutant simulation, where a salt bridge network matching the wild type is restored. Other important structural-dynamical properties, such as the trans-membrane helices mobility, analyzed via the principal component analysis, are similar for the wild type and double mutant while are different for the single mutant, providing a mechanistic explanation for their different functional properties. Copyright © 2010 Elsevier Inc. All rights reserved.

Structural basis for nuclear import complex dissociation by RanGTP.

PubMed

Lee, Soo Jae; Matsuura, Yoshiyuki; Liu, Sai Man; Stewart, Murray

2005-06-02

Nuclear protein import is mediated mainly by the transport factor importin-beta that binds cytoplasmic cargo, most often via the importin-alpha adaptor, and then transports it through nuclear pore complexes. This active transport is driven by disassembly of the import complex by nuclear RanGTP. The switch I and II loops of Ran change conformation with nucleotide state, and regulate its interactions with nuclear trafficking components. Importin-beta consists of 19 HEAT repeats that are based on a pair of antiparallel alpha-helices (referred to as the A- and B-helices). The HEAT repeats stack to yield two C-shaped arches, linked together to form a helicoidal molecule that has considerable conformational flexibility. Here we present the structure of full-length yeast importin-beta (Kap95p or karyopherin-beta) complexed with RanGTP, which provides a basis for understanding the crucial cargo-release step of nuclear import. We identify a key interaction site where the RanGTP switch I loop binds to the carboxy-terminal arch of Kap95p. This interaction produces a change in helicoidal pitch that locks Kap95p in a conformation that cannot bind importin-alpha or cargo. We suggest an allosteric mechanism for nuclear import complex disassembly by RanGTP.

A new kind of low-inductance transformer type magnetic switch (TTMS) with coaxial cylindrical conductors

NASA Astrophysics Data System (ADS)

Zhang, Yu; Liu, Jinliang

2013-02-01

As important devices for voltage boosting and switching, respectively, pulse transformer and magnetic switch are widely used in pulsed power technology. In this paper, a new kind of transformer type magnetic switch (TTMS) with coaxial cylindrical conductors is put forward to combine the functions of voltage boosting and switching in one power device. As a compact combination device of discrete pulse transformer and magnetic switch, the compact TTMS decreases the required volume of magnetic cores in a large scale. The primary windings of the TTMS have a parallel combination structure so that the TTMS which only has 3 turns of secondary windings has a step-up ratio at 1:9. Before the magnetic core saturates, the TTMS has low unsaturated inductances of windings and good pulse response characteristics, so it can be used to substitute the Marx generator to charge the pulse forming line (PFL) at the ranges of several hundred kV and several hundred ns. After the core saturates, the cylindrical conductors can decrease the saturated inductance of the secondary windings of TTMS to a level less than 400 nH. As a result, the proposed TTMS can be used as the boosting transformer and main switch of helical Blumlein PFL to form the quasi-square voltage pulse on the 160 Ω load with a short pulse rise time only at 60 ns.

A new kind of low-inductance transformer type magnetic switch (TTMS) with coaxial cylindrical conductors.

PubMed

Zhang, Yu; Liu, Jinliang

2013-02-01

As important devices for voltage boosting and switching, respectively, pulse transformer and magnetic switch are widely used in pulsed power technology. In this paper, a new kind of transformer type magnetic switch (TTMS) with coaxial cylindrical conductors is put forward to combine the functions of voltage boosting and switching in one power device. As a compact combination device of discrete pulse transformer and magnetic switch, the compact TTMS decreases the required volume of magnetic cores in a large scale. The primary windings of the TTMS have a parallel combination structure so that the TTMS which only has 3 turns of secondary windings has a step-up ratio at 1:9. Before the magnetic core saturates, the TTMS has low unsaturated inductances of windings and good pulse response characteristics, so it can be used to substitute the Marx generator to charge the pulse forming line (PFL) at the ranges of several hundred kV and several hundred ns. After the core saturates, the cylindrical conductors can decrease the saturated inductance of the secondary windings of TTMS to a level less than 400 nH. As a result, the proposed TTMS can be used as the boosting transformer and main switch of helical Blumlein PFL to form the quasi-square voltage pulse on the 160 Ω load with a short pulse rise time only at 60 ns.

Heterogeneity in iota-carrageenan molecular structure: insights for polymorph II→III transition in the presence of calcium ions

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

Janaswamy, Srinivas; Chandrasekaran, Rengaswami

2008-06-24

Iota-carrageenan is used in pharmaceutical and food applications due to its ability to complex with other hydrocolloids and proteins. Six distinct cation dependent allomorphs, consistent with its versatile functionality, have so far been observed in the solid state. In this contribution, X-ray structural details of calcium iota-carrageenan (form III) are reported. The polysaccharide retains the half-staggered, parallel, 3-fold, right-handed double helix stabilized by interchain hydrogen bonds from O-2H and O-6H in the Galp units. Results show that there are four helices, rather than one in I or three in II, organized in a larger pseudo-trigonal unit cell of dimensions a=27.44,more » c=13.01 A, and gamma=120 degrees . The four helices have similar core structures, but their sulfate group orientations are quite different. Fifteen calcium ions and 64 water molecules hold the helices together and promote helix-helix interactions. The results portray how the helices would shuffle around in an orchestrated manner to yield calcium iota-carrageenan III from II.« less

Effect of double-tailed surfactant architecture on the conformation, self-assembly, and processing in polypeptide-surfactant complexes.

PubMed

Junnila, Susanna; Hanski, Sirkku; Oakley, Richard J; Nummelin, Sami; Ruokolainen, Janne; Faul, Charl F J; Ikkala, Olli

2009-10-12

This work describes the solid-state conformational and structural properties of self-assembled polypeptide-surfactant complexes with double-tailed surfactants. Poly(L-lysine) was complexed with three dialkyl esters of phosphoric acid (i.e., phosphodiester surfactants), where the surfactant tail branching and length was varied to tune the supramolecular architecture in a facile way. After complexation with the branched surfactant bis(2-ethylhexyl) phosphate in an aqueous solution, the polypeptide chains adopted an alpha-helical conformation. These rod-like helices self-assembled into cylindrical phases with the amorphous alkyl tails pointing outward. In complexes with dioctyl phosphate and didodecyl phosphate, which have two linear n-octyl or n-dodecyl tails, respectively, the polypeptide formed antiparallel beta-sheets separated by alkyl layers, resulting in well-ordered lamellar self-assemblies. By heating, it was possible to trigger a partial opening of the beta-sheets and disruption of the lamellar phase. After repeated heating/cooling, all of these complexes also showed a glass transition between 37 and 50 degrees C. Organic solvent treatment and plasticization by overstoichiometric amount of surfactant led to structure modification in poly(L-lysine)-dioctyl phosphate complexes, PLL(diC8)(x) (x = 1.0-3.0). Here, the alpha-helical PLL is surrounded by the surfactants and these bottle-brush-like chains self-assemble in a hexagonal cylindrical morphology. As x is increased, the materials are clearly plasticized and the degree of ordering is improved: The stiff alpha-helical backbones in a softened surfactant matrix give rise to thermotropic liquid-crystalline phases. The complexes were examined by Fourier transform infrared spectroscopy, small- and wide-angle X-ray scattering, transmission electron microscopy, differential scanning calorimetry, polarized optical microscopy, and circular dichroism.

Dynamical control on helicity of electromagnetic waves by tunable metasurfaces

PubMed Central

Xu, He-Xiu; Sun, Shulin; Tang, Shiwei; Ma, Shaojie; He, Qiong; Wang, Guang-Ming; Cai, Tong; Li, Hai-Peng; Zhou, Lei

2016-01-01

Manipulating the polarization states of electromagnetic (EM) waves, a fundamental issue in optics, attracted intensive attention recently. However, most of the devices realized so far are either too bulky in size, and/or are passive with only specific functionalities. Here we combine theory and experiment to demonstrate that, a tunable metasurface incorporating diodes as active elements can dynamically control the reflection phase of EM waves, and thus exhibits unprecedented capabilities to manipulate the helicity of incident circular-polarized (CP) EM wave. By controlling the bias voltages imparted on the embedded diodes, we demonstrate that the device can work in two distinct states. Whereas in the “On” state, the metasurface functions as a helicity convertor and a helicity hybridizer within two separate frequency bands, it behaves as a helicity keeper within an ultra-wide frequency band in the “Off” state. Our findings pave the way to realize functionality-switchable devices related to phase control, such as frequency-tunable subwavelength cavities, anomalous reflectors and even holograms. PMID:27272350

Dynamical control on helicity of electromagnetic waves by tunable metasurfaces.

PubMed

Xu, He-Xiu; Sun, Shulin; Tang, Shiwei; Ma, Shaojie; He, Qiong; Wang, Guang-Ming; Cai, Tong; Li, Hai-Peng; Zhou, Lei

2016-06-08

Manipulating the polarization states of electromagnetic (EM) waves, a fundamental issue in optics, attracted intensive attention recently. However, most of the devices realized so far are either too bulky in size, and/or are passive with only specific functionalities. Here we combine theory and experiment to demonstrate that, a tunable metasurface incorporating diodes as active elements can dynamically control the reflection phase of EM waves, and thus exhibits unprecedented capabilities to manipulate the helicity of incident circular-polarized (CP) EM wave. By controlling the bias voltages imparted on the embedded diodes, we demonstrate that the device can work in two distinct states. Whereas in the "On" state, the metasurface functions as a helicity convertor and a helicity hybridizer within two separate frequency bands, it behaves as a helicity keeper within an ultra-wide frequency band in the "Off" state. Our findings pave the way to realize functionality-switchable devices related to phase control, such as frequency-tunable subwavelength cavities, anomalous reflectors and even holograms.

Colossal change in thermopower with temperature-driven p-n-type conduction switching in La x Sr2-x TiFeO6 double perovskites

NASA Astrophysics Data System (ADS)

Roy, Pinku; Maiti, Tanmoy

2018-02-01

Double perovskite materials have been studied in detail by many researchers, as their magnetic and electronic properties can be controlled by the substitution of alkaline earth metals or lanthanides in the A site and transition metals in the B site. Here we report the temperature-driven, p-n-type conduction switching assisted, large change in thermopower in La3+-doped Sr2TiFeO6-based double perovskites. Stoichiometric compositions of La x Sr2-x TiFeO6 (LSTF) with 0  ⩽  x  ⩽  0.25 were synthesized by the solid-state reaction method. Rietveld refinement of room-temperature XRD data confirmed a single-phase solid solution with cubic crystal structure and Pm\\bar{3}m space group. From temperature-dependent electrical conductivity and Seebeck coefficient (S) studies it is evident that all the compositions underwent an intermediate semiconductor-to-metal transition before the semiconductor phase reappeared at higher temperature. In the process of semiconductor-metal-semiconductor transition, LSTF compositions demonstrated temperature-driven p-n-type conduction switching behavior. The electronic restructuring which occurs due to the intermediate metallic phase between semiconductor phases leads to the colossal change in S for LSTF oxides. The maximum drop in thermopower (ΔS ~ 2516 µV K-1) was observed for LSTF with x  =  0.1 composition. Owing to their enormous change in thermopower of the order of millivolts per kelvin, integrated with p-n-type resistance switching, these double perovskites can be used for various high-temperature multifunctional device applications such as diodes, sensors, switches, thermistors, thyristors, thermal runaway monitors etc. Furthermore, the conduction mechanisms of these oxides were explained by the small polaron hopping model.

Low current extended duration spark ignition system

DOEpatents

Waters, Stephen Howard; Chan, Anthony Kok-Fai

2005-08-30

A system for firing a spark plug is disclosed. The system includes a timing controller configured to send a first timing signal and a second timing signal. The system also includes an ignition transformer having a primary winding and a secondary winding and a spark-plug that is operably associated with the secondary winding. A first switching element is disposed between the timing controller and the primary winding of the ignition transformer. The first switching element controls a supply of power to the primary winding based on the first timing signal. Also, a second switching element is disposed between the timing controller and the primary winding of the ignition transformer. The second switching element controls the supply of power to the primary winding based on the second timing signal. A method for firing a spark plug is also disclosed.

Double helix boron-10 powder thermal neutron detector

DOEpatents

Wang, Zhehui; Morris, Christopher L.; Bacon, Jeffrey D.

2015-06-02

A double-helix Boron-10 powder detector having intrinsic thermal neutron detection efficiency comparable to 36'' long, 2-in diameter, 2-bar Helium-3 detectors, and which can be used to replace such detectors for use in portal monitoring, is described. An embodiment of the detector includes a metallic plate coated with Boron-10 powder for generating alpha and Lithium-7 particles responsive to neutrons impinging thereon supported by insulators affixed to at least two opposing edges; a grounded first wire wound in a helical manner around two opposing insulators; and a second wire having a smaller diameter than that of the first wire, wound in a helical manner around the same insulators and spaced apart from the first wire, the second wire being positively biased. A gas, disposed within a gas-tight container enclosing the plate, insulators and wires, and capable of stopping alpha and Lithium-7 particles and generating electrons produces a signal on the second wire which is detected and subsequently related to the number of neutrons impinging on the plate.

HolT Hunter: Software for Identifying and Characterizing Low-Strain DNA Holliday Triangles

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

Sherman W. B.

2012-06-05

Synthetic DNA nanostructures are most commonly held together via Holliday junctions. These junctions allow for a wide variety of different angles between the double helices they connect. Nevertheless, only constructs with a very limited selection of angles have been built, to date, because of the computational complexity of identifying structures that fit together with low strain at odd angles. I have developed an algorithm that finds over 95% of the possible solutions by breaking the problem down into two portions. First, there is a problem of how smooth rods can form triangles by lying across one another. This problem ismore » easily handled by numerical computation. Second, there is the question of how distorted DNA double helices would need to be to fit onto the rod structure. This strain is calculated directly. The algorithm has been implemented in a Mathematica 8 notebook called Holliday Triangle Hunter. A large database of solutions has been identified. Additional interface software is available to facilitate drawing and viewing models.« less

Sequential power-up circuit

DOEpatents

Kronberg, James W.

1992-01-01

A sequential power-up circuit for starting several electrical load elements in series to avoid excessive current surge, comprising a voltage ramp generator and a set of voltage comparators, each comparator having a different reference voltage and interfacing with a switch that is capable of turning on one of the load elements. As the voltage rises, it passes the reference voltages one at a time and causes the switch corresponding to that voltage to turn on its load element. The ramp is turned on and off by a single switch or by a logic-level electrical signal. The ramp rate for turning on the load element is relatively slow and the rate for turning the elements off is relatively fast. Optionally, the duration of each interval of time between the turning on of the load elements is programmable.

Electronic Switch Arrays for Managing Microbattery Arrays

NASA Technical Reports Server (NTRS)

Mojarradi, Mohammad; Alahmad, Mahmoud; Sukumar, Vinesh; Zghoul, Fadi; Buck, Kevin; Hess, Herbert; Li, Harry; Cox, David

2008-01-01

Integrated circuits have been invented for managing the charging and discharging of such advanced miniature energy-storage devices as planar arrays of microscopic energy-storage elements [typically, microscopic electrochemical cells (microbatteries) or microcapacitors]. The architecture of these circuits enables implementation of the following energy-management options: dynamic configuration of the elements of an array into a series or parallel combination of banks (subarrarys), each array comprising a series of parallel combination of elements; direct addressing of individual banks for charging/or discharging; and, disconnection of defective elements and corresponding reconfiguration of the rest of the array to utilize the remaining functional elements to obtain the desited voltage and current performance. An integrated circuit according to the invention consists partly of a planar array of field-effect transistors that function as switches for routing electric power among the energy-storage elements, the power source, and the load. To connect the energy-storage elements to the power source for charging, a specific subset of switches is closed; to connect the energy-storage elements to the load for discharging, a different specific set of switches is closed. Also included in the integrated circuit is circuitry for monitoring and controlling charging and discharging. The control and monitoring circuitry, the switching transistors, and interconnecting metal lines are laid out on the integrated-circuit chip in a pattern that registers with the array of energy-storage elements. There is a design option to either (1) fabricate the energy-storage elements in the corresponding locations on, and as an integral part of, this integrated circuit; or (2) following a flip-chip approach, fabricate the array of energy-storage elements on a separate integrated-circuit chip and then align and bond the two chips together.

The guanine nucleotide exchange factor Ric-8A induces domain separation and Ras domain plasticity in Gαi1

PubMed Central

Van Eps, Ned; Thomas, Celestine J.; Hubbell, Wayne L.; Sprang, Stephen R.

2015-01-01

Heterotrimeric G proteins are activated by exchange of GDP for GTP at the G protein alpha subunit (Gα), most notably by G protein-coupled transmembrane receptors. Ric-8A is a soluble cytoplasmic protein essential for embryonic development that acts as both a guanine nucleotide exchange factor (GEF) and a chaperone for Gα subunits of the i, q, and 12/13 classes. Previous studies demonstrated that Ric-8A stabilizes a dynamically disordered state of nucleotide-free Gα as the catalytic intermediate for nucleotide exchange, but no information was obtained on the structures involved or the magnitude of the structural fluctuations. In the present study, site-directed spin labeling (SDSL) together with double electron-electron resonance (DEER) spectroscopy is used to provide global distance constraints that identify discrete members of a conformational ensemble in the Gαi1:Ric-8A complex and the magnitude of structural differences between them. In the complex, the helical and Ras-like nucleotide-binding domains of Gαi1 pivot apart to occupy multiple resolved states with displacements as large as 25 Å. The domain displacement appears to be distinct from that observed in Gαs upon binding of Gs to the β2 adrenergic receptor. Moreover, the Ras-like domain exhibits structural plasticity within and around the nucleotide-binding cavity, and the switch I and switch II regions, which are known to adopt different conformations in the GDP- and GTP-bound states of Gα, undergo structural rearrangements. Collectively, the data show that Ric-8A induces a conformationally heterogeneous state of Gαi and provide insight into the mechanism of action of a nonreceptor Gα GEF. PMID:25605908

Silicon Carbide (SiC) MOSFET-based Full-Bridge for Fusion Science Applications

NASA Astrophysics Data System (ADS)

Ziemba, Timothy; Miller, Kenneth; Prager, James; Picard, Julian; Hashim, Akel

2014-10-01

Switching power amplifiers (SPAs) have a wide variety of applications within the fusion science community, including feedback and control systems for dynamic plasma stabilization in tokamaks, inductive and arc plasma sources, Radio Frequency (RF) helicity and flux injection, RF plasma heating and current drive schemes, ion beam generation, and RF pre-ionizer systems. SiC MOSFETs offer many advantages over IGBTs including lower drive energy requirements, lower conduction and switching losses, and higher switching frequency capabilities. When comparing SiC and traditional silicon-based MOSFETs, SiC MOSFETs provide higher current carrying capability allowing for smaller package weights and sizes and lower operating temperature. Eagle Harbor Technologies (EHT) is designing, constructing, and testing a SiC MOSFET-based full-bridge SPA. EHT will leverage the proprietary gate drive technology previously developed with the support of a DOE SBIR, which will enable fast, efficient switching in a small form factor. The primary goal is to develop a SiC MOSFET-based SPA for fusion science applications. Work supported in part by the DOE under Contract Number DE-SC0011907.

Efficient single-mode operation of a cladding-pumped ytterbium-doped helical-core fiber laser.

PubMed

Wang, P; Cooper, L J; Sahu, J K; Clarkson, W A

2006-01-15

A novel approach to achieving robust single-spatial-mode operation of cladding-pumped fiber lasers with multimode cores is reported. The approach is based on the use of a fiber geometry in which the core has a helical trajectory within the inner cladding to suppress laser oscillation on higher-order modes. In a preliminary proof-of-principle study, efficient single-mode operation of a cladding-pumped ytterbium-doped helical-core fiber laser with a 30 microm diameter core and a numerical aperture of 0.087 has been demonstrated. The laser yielded 60.4 W of output at 1043 nm in a beam with M2 < 1.4 for 92.6 W launched pump power from a diode stack at 976 nm. The slope efficiency at pump powers well above threshold was approximately 84%, which compares favorably with the slope efficiencies achievable with conventional straight-core Yb-doped double-clad fiber lasers.

Pyrolysis of Helical Coordination Polymers for Metal-Sulfide-Based Helices with Broadband Chiroptical Activity.

PubMed

Hirai, Kenji; Yeom, Bongjun; Sada, Kazuki

2017-06-27

Fabrication of chiroptical materials with broadband response in the visible light region is vital to fully realize their potential applications. One way to achieve broadband chiroptical activity is to fabricate chiral nanostructures from materials that exhibit broadband absorption in the visible light region. However, the compounds used for chiroptical materials have predominantly been limited to materials with narrowband spectral response. Here, we synthesize Ag 2 S-based nanohelices derived from helical coordination polymers. The right- and left-handed coordination helices used as precursors are prepared from l- and d-glutathione with Ag + and a small amount of Cu 2+ . The pyrolysis of the coordination helices yields right- and left-handed helices of Cu 0.12 Ag 1.94 S/C, which exhibit chiroptical activity spanning the entire visible light region. Finite element method simulations substantiate that the broadband chiroptical activity is attributed to synergistic broadband light absorption and light scattering. Furthermore, another series of Cu 0.10 Ag 1.90 S/C nanohelices are synthesized by choosing the l- or d-Glu-Cys as starting materials. The pitch length of nanohelicies is controlled by changing the peptides, which alters their chiroptical properties. The pyrolysis of coordination helices enables one to fabricate helical Ag 2 S-based materials that enable broadband chiroptical activity but have not been explored owing to the lack of synthetic routes.

Topping cycle for coal-fueled electric power plants using the ceramic helical expander

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

Myers, B.; Landingham, R.; Mohr, P.

Ceramic helical expanders are advocated as the work output element in a 2500/sup 0/F direct coal-fired Brayton topping cycle for central power station application. When combined with a standard steam electric power plant cycle, such a cycle could result in an overall thermal conversion efficiency in excess of 50 percent. The performance, coal tolerance, and system-development-time advantages of the ceramic helical expander approach are enumerated. A perspective on the choice of design and materials is provided. A preliminary consideration of physical properties, economic questions, and service experience has led us to a preference for the silicon nitride and silicon carbidemore » family of materials. A program to confirm the performance and coal tolerance aspects of a ceramic helical expander system is planned.« less

A transcriptional serenAID: the role of noncoding RNAs in class switch recombination

PubMed Central

Yewdell, William T.; Chaudhuri, Jayanta

2017-01-01

Abstract During an immune response, activated B cells may undergo class switch recombination (CSR), a molecular rearrangement that allows B cells to switch from expressing IgM and IgD to a secondary antibody heavy chain isotype such as IgG, IgA or IgE. Secondary antibody isotypes provide the adaptive immune system with distinct effector functions to optimally combat various pathogens. CSR occurs between repetitive DNA elements within the immunoglobulin heavy chain (Igh) locus, termed switch (S) regions and requires the DNA-modifying enzyme activation-induced cytidine deaminase (AID). AID-mediated DNA deamination within S regions initiates the formation of DNA double-strand breaks, which serve as biochemical beacons for downstream DNA repair pathways that coordinate the ligation of DNA breaks. Myriad factors contribute to optimal AID targeting; however, many of these factors also localize to genomic regions outside of the Igh locus. Thus, a current challenge is to explain the specific targeting of AID to the Igh locus. Recent studies have implicated noncoding RNAs in CSR, suggesting a provocative mechanism that incorporates Igh-specific factors to enable precise AID targeting. Here, we chronologically recount the rich history of noncoding RNAs functioning in CSR to provide a comprehensive context for recent and future discoveries. We present a model for the RNA-guided targeting of AID that attempts to integrate historical and recent findings, and highlight potential caveats. Lastly, we discuss testable hypotheses ripe for current experimentation, and explore promising ideas for future investigations. PMID:28535205

MicroRNAs Form Triplexes with Double Stranded DNA at Sequence-Specific Binding Sites; a Eukaryotic Mechanism via which microRNAs Could Directly Alter Gene Expression

PubMed Central

Grace, Christy R.; Ferreira, Antonio M.; Waddell, M. Brett; Ridout, Granger; Naeve, Deanna; Leuze, Michael; LoCascio, Philip F.; Panetta, John C.; Wilkinson, Mark R.; Pui, Ching-Hon; Naeve, Clayton W.; Uberbacher, Edward C.; Bonten, Erik J.; Evans, William E.

2016-01-01

MicroRNAs are important regulators of gene expression, acting primarily by binding to sequence-specific locations on already transcribed messenger RNAs (mRNA) and typically down-regulating their stability or translation. Recent studies indicate that microRNAs may also play a role in up-regulating mRNA transcription levels, although a definitive mechanism has not been established. Double-helical DNA is capable of forming triple-helical structures through Hoogsteen and reverse Hoogsteen interactions in the major groove of the duplex, and we show physical evidence (i.e., NMR, FRET, SPR) that purine or pyrimidine-rich microRNAs of appropriate length and sequence form triple-helical structures with purine-rich sequences of duplex DNA, and identify microRNA sequences that favor triplex formation. We developed an algorithm (Trident) to search genome-wide for potential triplex-forming sites and show that several mammalian and non-mammalian genomes are enriched for strong microRNA triplex binding sites. We show that those genes containing sequences favoring microRNA triplex formation are markedly enriched (3.3 fold, p<2.2 × 10−16) for genes whose expression is positively correlated with expression of microRNAs targeting triplex binding sequences. This work has thus revealed a new mechanism by which microRNAs could interact with gene promoter regions to modify gene transcription. PMID:26844769

Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids

PubMed Central

Iqbal, Asif; Arslan, Sinan; Okumus, Burak; Wilson, Timothy J.; Giraud, Gerard; Norman, David G.; Ha, Taekjip; Lilley, David M. J.

2008-01-01

We have found that the efficiency of fluorescence resonance energy transfer between Cy3 and Cy5 terminally attached to the 5′ ends of a DNA duplex is significantly affected by the relative orientation of the two fluorophores. The cyanine fluorophores are predominantly stacked on the ends of the helix in the manner of an additional base pair, and thus their relative orientation depends on the length of the helix. Observed fluorescence resonance energy transfer (FRET) efficiency depends on the length of the helix, as well as its helical periodicity. By changing the helical geometry from B form double-stranded DNA to A form hybrid RNA/DNA, a marked phase shift occurs in the modulation of FRET efficiency with helix length. Both curves are well explained by the standard geometry of B and A form helices. The observed modulation for both polymers is less than that calculated for a fully rigid attachment of the fluorophores. However, a model involving lateral mobility of the fluorophores on the ends of the helix explains the observed experimental data. This has been further modified to take account of a minor fraction of unstacked fluorophore observed by fluorescent lifetime measurements. Our data unequivocally establish that Förster transfer obeys the orientation dependence as expected for a dipole–dipole interaction. PMID:18676615

Helicity-dependent cross sections and double-polarization observable E in η photoproduction from quasifree protons and neutrons

NASA Astrophysics Data System (ADS)

Witthauer, L.; Dieterle, M.; Abt, S.; Achenbach, P.; Afzal, F.; Ahmed, Z.; Akondi, C. S.; Annand, J. R. M.; Arends, H. J.; Bashkanov, M.; Beck, R.; Biroth, M.; Borisov, N. S.; Braghieri, A.; Briscoe, W. J.; Cividini, F.; Costanza, S.; Collicott, C.; Denig, A.; Downie, E. J.; Drexler, P.; Ferretti-Bondy, M. I.; Gardner, S.; Garni, S.; Glazier, D. I.; Glowa, D.; Gradl, W.; Günther, M.; Gurevich, G. M.; Hamilton, D.; Hornidge, D.; Huber, G. M.; Käser, A.; Kashevarov, V. L.; Kay, S.; Keshelashvili, I.; Kondratiev, R.; Korolija, M.; Krusche, B.; Lazarev, A. B.; Linturi, J. M.; Lisin, V.; Livingston, K.; Lutterer, S.; MacGregor, I. J. D.; Mancell, J.; Manley, D. M.; Martel, P. P.; Metag, V.; Meyer, W.; Miskimen, R.; Mornacchi, E.; Mushkarenkov, A.; Neganov, A. B.; Neiser, A.; Oberle, M.; Ostrick, M.; Otte, P. B.; Paudyal, D.; Pedroni, P.; Polonski, A.; Prakhov, S. N.; Rajabi, A.; Reicherz, G.; Ron, G.; Rostomyan, T.; Sarty, A.; Sfienti, C.; Sikora, M. H.; Sokhoyan, V.; Spieker, K.; Steffen, O.; Strakovsky, I. I.; Strub, Th.; Supek, I.; Thiel, A.; Thiel, M.; Thomas, A.; Unverzagt, M.; Usov, Yu. A.; Wagner, S.; Walford, N. K.; Watts, D. P.; Werthmüller, D.; Wettig, J.; Wolfes, M.; Zana, L.; A2 Collaboration at MAMI

2017-05-01

Precise helicity-dependent cross sections and the double-polarization observable E were measured for η photoproduction from quasifree protons and neutrons bound in the deuteron. The η →2 γ and η →3 π0→6 γ decay modes were used to optimize the statistical quality of the data and to estimate systematic uncertainties. The measurement used the A2 detector setup at the tagged photon beam of the electron accelerator MAMI in Mainz. A longitudinally polarized deuterated butanol target was used in combination with a circularly polarized photon beam from bremsstrahlung of a longitudinally polarized electron beam. The reaction products were detected with the electromagnetic calorimeters Crystal Ball and TAPS, which covered 98% of the full solid angle. The results show that the narrow structure observed earlier in the unpolarized excitation function of η photoproduction off the neutron appears only in reactions with antiparallel photon and nucleon spin (σ1 /2). It is absent for reactions with parallel spin orientation (σ3 /2) and thus very probably related to partial waves with total spin 1/2. The behavior of the angular distributions of the helicity-dependent cross sections was analyzed by fitting them withLegendre polynomials. The results are in good agreement with a model from the Bonn-Gatchina group, which uses an interference of P11 and S11 partial waves to explain the narrow structure.

Watt-level passively Q-switched double-cladding fiber laser based on graphene oxide saturable absorber.

PubMed

Yu, Zhenhua; Song, Yanrong; Dong, Xinzheng; Li, Yanlin; Tian, Jinrong; Wang, Yonggang

2013-10-10

A watt-level passively Q-switched ytterbium-doped double-cladding fiber laser with a graphene oxide (GO) absorber was demonstrated. The structure of the GO saturable absorber mirror (GO-SAM) was of the sandwich type. A maximum output power of 1.8 W was obtained around a wavelength of 1044 nm. To the best of our knowledge, this is the highest output power in Q-switched fiber lasers based on a GO saturable absorber. The pure GO was protected from the oxygen in the air so that the damage threshold of the GO-SAM was effectively raised. The gain fiber was a D-shaped ytterbium-doped double-cladding fiber. The pulse repetition rates were tuned from 120 to 215 kHz with pump powers from 3.89 to 7.8 W. The maximum pulse energy was 8.37 μJ at a pulse width of 1.7 μs.

Creating Directed Double-strand Breaks with the Ref Protein: A Novel Rec A-Dependent Nuclease from Bacteriophage P1

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

Gruenig, Marielle C.; Lu, Duo; Won, Sang Joon

2012-03-16

The bacteriophage P1-encoded Ref protein enhances RecA-dependent recombination in vivo by an unknown mechanism. We demonstrate that Ref is a new type of enzyme; that is, a RecA-dependent nuclease. Ref binds to ss- and dsDNA but does not cleave any DNA substrate until RecA protein and ATP are added to form RecA nucleoprotein filaments. Ref cleaves only where RecA protein is bound. RecA functions as a co-nuclease in the Ref/RecA system. Ref nuclease activity can be limited to the targeted strands of short RecA-containing D-loops. The result is a uniquely programmable endonuclease activity, producing targeted double-strand breaks at any chosenmore » DNA sequence in an oligonucleotide-directed fashion. We present evidence indicating that cleavage occurs in the RecA filament groove. The structure of the Ref protein has been determined to 1.4 {angstrom} resolution. The core structure, consisting of residues 77-186, consists of a central 2-stranded {beta}-hairpin that is sandwiched between several {alpha}-helical and extended loop elements. The N-terminal 76 amino acid residues are disordered; this flexible region is required for optimal activity. The overall structure of Ref, including several putative active site histidine residues, defines a new subclass of HNH-family nucleases. We propose that enhancement of recombination by Ref reflects the introduction of directed, recombinogenic double-strand breaks.« less

Ion-barrier for memristors/ReRAM and methods thereof

DOEpatents

Haase, Gad S.

2017-11-28

The present invention relates to memristive devices including a resistance-switching element and a barrier element. In particular examples, the barrier element is a monolayer of a transition metal chalcogenide that sufficiently inhibits diffusion of oxygen atoms or ions out of the switching element. As the location of these atoms and ions determine the state of the device, inhibiting diffusion would provide enhanced state retention and device reliability. Other types of barrier elements, as well as methods for forming such elements, are described herein.

NETWORK SYNTHESIS OF CASCADED THRESHOLD ELEMENTS.

DTIC Science & Technology

A threshold function is a switching function which can be stimulated by a single, simplified, idealized neuron, or threshold element. In this report... threshold functions are examined in the context of abstract set theory and linear algebra for the purpose of obtaining practical synthesis procedures...for networks of threshold elements. A procedure is described by which, for any given switching function, a cascade network of these elements can be

Bilingual Voicing: A Study of Code-Switching in the Reported Speech of Finnish Immigrants in Estonia

ERIC Educational Resources Information Center

Frick, Maria; Riionheimo, Helka

2013-01-01

Through a conversation analytic investigation of Finnish-Estonian bilingual (direct) reported speech (i.e., voicing) by Finns who live in Estonia, this study shows how code-switching is used as a double contextualization device. The code-switched voicings are shaped by the on-going interactional situation, serving its needs by opening up a context…

A low-loss, single-pole, four-throw RF MEMS switch driven by a double stop comb drive

NASA Astrophysics Data System (ADS)

Kang, S.; Kim, H. C.; Chun, K.

2009-03-01

Our goal was to develop a single-pole four-throw (SP4T) radio frequency microelectromechanical system (RF MEMS) switch for band selection in a multi-band, multi-mode, front-end module of a wireless transceiver system. The SP4T RF MEMS switch was based on an arrangement of four single-pole single-throw (SPST) RF MEMS switches. The SP4T RF MEMS switch was driven by a double stop (DS) comb drive, with a lateral resistive contact, and composed of single crystalline silicon (SCS) on glass. A large contact force at a low-drive voltage was achieved by electrostatic actuation of the DS comb drive. Good RF characteristics were achieved by the large contact force and the lateral resistive Au-to-Au contact. Mechanical reliability was achieved by using SCS which has no residual stress as a structure material. The developed SP4T RF MEMS switch has a drive voltage of 15 V, an insertion loss below 0.31 dB at 6 GHz after more than one million cycles under a 10 mW signal, a return loss above 20 dB and an isolation value above 36 dB.

OVERMODED HIGH-POWER RF MAGNETIC SWITCHES AND CIRCULATORS

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

Tantawi, Sami

2002-08-20

We present design methodology for active rf magnetic components which are suitable for pulse compression systems of future X-band linear colliders. These components comprise an array of active elements arranged together so that the total electromagnetic field is reduced and the power handling capabilities are increased. The active element of choice is a magnetic material (garnet), which can be switched by changing a biasing magnetic field. A novel design allows these components to operate in the low loss circular waveguide mode TE{sub 01}. We describe the design methodology, the switching elements and circuits.

Best packing of identical helices

NASA Astrophysics Data System (ADS)

Huh, Youngsik; Hong, Kyungpyo; Kim, Hyoungjun; No, Sungjong; Oh, Seungsang

2016-10-01

In this paper we prove the unique existence of a ropelength-minimizing conformation of the θ-spun double helix in a mathematically rigorous way, and find the minimal ropelength {{{Rop}}}* (θ )=-\\tfrac{8π }{t} where t is the unique solution in [-θ ,0] of the equation 2-2\\cos (t+θ )={t}2. Using this result, the pitch angles of the standard, triple and quadruple helices are around 39.3771^\\circ , 42.8354^\\circ and 43.8351^\\circ , respectively, which are almost identical with the approximated pitch angles of the zero-twist structures previously known by Olsen and Bohr. We also find the ropelength of the standard N-helix.

Switch Rates During Acute Treatment for Bipolar II Depression With Lithium, Sertraline, or the Two Combined: A Randomized Double-Blind Comparison.

PubMed

Altshuler, Lori L; Sugar, Catherine A; McElroy, Susan L; Calimlim, Brian; Gitlin, Michael; Keck, Paul E; Aquino-Elias, Ana; Martens, Brian E; Fischer, E Grace; English, Teri L; Roach, Janine; Suppes, Trisha

2017-03-01

The authors compared medication-induced mood switch risk (primary outcome), as well as treatment response and side effects (secondary outcomes) with three acute-phase treatments for bipolar II depression. In a 16-week, double-blind, multisite comparison study, 142 participants with bipolar II depression were randomly assigned to receive lithium monotherapy (N=49), sertraline monotherapy (N=45), or combination treatment with lithium and sertraline (N=48). At each visit, mood was assessed using standardized rating scales. Rates of switch were compared, as were rates of treatment response and the presence and severity of treatment-emergent side effects. Twenty participants (14%) experienced a switch during the study period (hypomania, N=17; severe hypomania, N=3). Switch rates did not differ among the three treatment groups, even after accounting for dropout. No patient had a manic switch or was hospitalized for a switch. Most switches occurred within the first 5 weeks of treatment. The treatment response rate for the overall sample was 62.7% (N=89), without significant differences between groups after accounting for dropout. The lithium/sertraline combination group had a significantly higher overall dropout rate than the monotherapy groups but did not have an accelerated time to response. Lithium monotherapy, sertraline monotherapy, and lithium/sertraline combination therapy were associated with similar switch and treatment response rates in participants with bipolar II depression. The dropout rate was higher in the lithium/sertraline combination treatment group, without any treatment acceleration advantage.

Evaluation of Plastic Media Blasting Equipment

DTIC Science & Technology

1987-04-01

the differential pressure across the filter element or by a timer with a differential pressure switch override. The timer and the differential pressure ...automatic. The mechanism should be activated by the differential pressure across the filter element or by a timer with a differential pressure switch override...The timer and the differential pressure switch settings should be adjustable. The dust then falls to the bottom of the baghouse for

Simplification of the helical TEN2 laser

NASA Astrophysics Data System (ADS)

Krahn, K.-H.

1980-04-01

The observation that the helical TEN2 laser can effectively be simplified by giving up the use of decoupling elements as well as by abolishing the segmentation of the electrode structure is examined. Although, as a consequence of this simplification, the operating pressure range was slightly decreased, the output power could be improved by roughly 30%, a result which is attributed to the new electrode geometry exhibiting lower inductance and lower damping losses.

Sequential power-up circuit

DOEpatents

Kronberg, J.W.

1992-06-02

A sequential power-up circuit for starting several electrical load elements in series to avoid excessive current surge, comprising a voltage ramp generator and a set of voltage comparators, each comparator having a different reference voltage and interfacing with a switch that is capable of turning on one of the load elements. As the voltage rises, it passes the reference voltages one at a time and causes the switch corresponding to that voltage to turn on its load element. The ramp is turned on and off by a single switch or by a logic-level electrical signal. The ramp rate for turning on the load element is relatively slow and the rate for turning the elements off is relatively fast. Optionally, the duration of each interval of time between the turning on of the load elements is programmable. 2 figs.

Magnetic elements for switching magnetization magnetic force microscopy tips.

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

Cambel, V.; Elias, P.; Gregusova, D.

2010-09-01

Using combination of micromagnetic calculations and magnetic force microscopy (MFM) imaging we find optimal parameters for novel magnetic tips suitable for switching magnetization MFM. Switching magnetization MFM is based on two-pass scanning atomic force microscopy with reversed tip magnetization between the scans. Within the technique the sum of the scanned data with reversed tip magnetization depicts local atomic forces, while their difference maps the local magnetic forces. Here we propose the design and calculate the magnetic properties of tips suitable for this scanning probe technique. We find that for best performance the spin-polarized tips must exhibit low magnetic moment, lowmore » switching fields, and single-domain state at remanence. The switching field of such tips is calculated and optimum shape of the Permalloy elements for the tips is found. We show excellent correspondence between calculated and experimental results for Py elements.« less

Ratios of helicity amplitudes for exclusive ρ 0 electroproduction on transversely polarized protons

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

Airapetian, A.; Akopov, N.; Akopov, Z.

Exclusive ρ 0-meson electroproduction is studied by the HERMES experiment, using the 27.6 GeV longitudinally polarized electron/positron beam of HERA and a transversely polarized hydrogen target, in the kinematic region 1.0 GeV 2 < Q 2 < 7.0 GeV 2, 3.0 GeV < W < 6.3 GeV, and –t' < 0.4 GeV 2. Using an unbinned maximum-likelihood method, 25 parameters are extracted. These determine the real and imaginary parts of the ratios of several helicity amplitudes describing ρ 0-meson production by a virtual photon. The denominator of those ratios is the dominant amplitude, the nucleon-helicity-non-flip amplitude F 01/201/2, which describesmore » the production of a longitudinal ρ 0-meson by a longitudinal virtual photon. The ratios of nucleon-helicity-non-flip amplitudes are found to be in good agreement with those from the previous HERMES analysis. The transverse target polarization allows for the first time the extraction of ratios of a number of nucleon-helicity-flip amplitudes to F 01/201/2. Results obtained in a handbag approach based on generalized parton distributions taking into account the contribution from pion exchange are found to be in good agreement with these ratios. Within the model, the data favor a positive sign for the π - ρ transition form factor. By also exploiting the longitudinal beam polarization, a total of 71 ρ 0 spin-density matrix elements is determined from the extracted 25 parameters, in contrast to only 53 elements as directly determined in earlier analyses.« less

Ratios of helicity amplitudes for exclusive ρ 0 electroproduction on transversely polarized protons

DOE PAGES

Airapetian, A.; Akopov, N.; Akopov, Z.; ...

2017-06-08

Exclusive ρ 0-meson electroproduction is studied by the HERMES experiment, using the 27.6 GeV longitudinally polarized electron/positron beam of HERA and a transversely polarized hydrogen target, in the kinematic region 1.0 GeV 2 < Q 2 < 7.0 GeV 2, 3.0 GeV < W < 6.3 GeV, and –t' < 0.4 GeV 2. Using an unbinned maximum-likelihood method, 25 parameters are extracted. These determine the real and imaginary parts of the ratios of several helicity amplitudes describing ρ 0-meson production by a virtual photon. The denominator of those ratios is the dominant amplitude, the nucleon-helicity-non-flip amplitude F 01/201/2, which describesmore » the production of a longitudinal ρ 0-meson by a longitudinal virtual photon. The ratios of nucleon-helicity-non-flip amplitudes are found to be in good agreement with those from the previous HERMES analysis. The transverse target polarization allows for the first time the extraction of ratios of a number of nucleon-helicity-flip amplitudes to F 01/201/2. Results obtained in a handbag approach based on generalized parton distributions taking into account the contribution from pion exchange are found to be in good agreement with these ratios. Within the model, the data favor a positive sign for the π - ρ transition form factor. By also exploiting the longitudinal beam polarization, a total of 71 ρ 0 spin-density matrix elements is determined from the extracted 25 parameters, in contrast to only 53 elements as directly determined in earlier analyses.« less

Double-injection, deep-impurity switch development

NASA Technical Reports Server (NTRS)

Whitson, D. W.

1985-01-01

The overall objective of this program was the development of device design and process techniques for the fabrication of a double-injection, deep-impurity (DI) sup 2 silicon switch that operates in the 2-10 kV range with conduction current values of 5 A at 2 kV and 1 A at 10 kV. Other major specifications include a holding voltage of 10 V with no gate current, 10 microsec switching time, and power dissipation of 50 W at 75 C. It was decided to concentrate on the lateral circular devices in order to optimize the gold diffusion. This resulted in devices that are much better switches (approx.1 micro sec switching time), and in a gold diffusion process that is much more controllable than those previously developed. Some results with injection-gated devices were also obtained. The current conduction for V less than VT was analyzed and seen to agree, for the most part, with Lampert's theory. Various sections of this report describe the device designs, wafer-processing techniques, and various measurements which include ac and dc characteristics and four-point probe.

The results of a two-stage double switch operation for congenital corrected transposition of the great arteries with a deconditioned morphologically left ventricle.

PubMed

Cui, Bin; Li, Shoujun; Yan, Jun; Shen, Xiangdong; Wang, Xu; Yang, Keming; Hua, Zhongdong; Wang, Qiang; Tian, Meice

2014-12-01

The purpose of this retrospective study was to evaluate a two-stage double switch operation, morphological left ventricular (mLV) retraining followed by an atrial-arterial switch operation, in the management of patients with congenitally corrected transposition of the great arteries (CCTGA) and a deconditioned mLV. Between May 2005 and May 2011, 14 patients with CCTGA and a deconditioned mLV anomaly underwent the two-stage double switch operation. There were eight males and six females aged between 2.5 and 72 months (mean: 34.4 ± 24.0 months) old and weighing from 5 to 23 kg (mean: 12.7 ± 4.9 kg). The major associated malformations included: tricuspid regurgitation (TR, n = 13); restrictive ventricular septal defect (n = 10); atrial septal defect or patent foramen ovale (n = 7); mild pulmonary stenosis (n = 5) and patent ductus arteriosus (n = 4). These patients underwent morphological left ventricular retraining by means of pulmonary artery banding under general anaesthesia, which was then followed by a double switch operation under general anaesthesia and cardiopulmonary bypass. There were no deaths or complications during the hospital stay or follow-up for the mLV retraining. In comparison with preoperative conditions, the mLV end-diastolic diameter (mLVEDd), the posterior wall thickness of the mLV and the mLV/mRV pressure ratio were all increased; the interventricular septum had moved partially to the midline position and TR had decreased. After the atrial-arterial switch procedure, 2 patients died during the perioperative period. The causes of death included serious cardiac arrhythmia with circulatory collapse and sudden death. The others were followed up for 2-8 years: 1 patient died from serious cardiac arrhythmias with circulatory collapse in the follow-up period. With regard to the others, 8 were evaluated as New York Heart Association Functional Class I, and the other 3 as Class II. Moderate aortic valve regurgitation was noted in 3 patients and moderate mitral regurgitation in 1 patient. For CCTGA children with degraded mLV, the two-stage double switch procedure can be performed with low mortality and morbidity and may be an appealing alternative to conventional repair. mLV retraining should be performed as early as possible. The second-stage atrial-arterial switch procedure showed satisfactory early and mid-term results. More attention should be paid to the long-term function of the mLV and the aortic valve. © The Author 2014. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

AN ANGIOTENSIN II TYPE 1 RECEPTOR ACTIVATION SWITCH PATCH REVEALED THROUGH EVOLUTIONARY TRACE ANALYSIS

PubMed Central

Bonde, Marie Mi; Yao, Rong; Ma, Jian-Nong; Madabushi, Srinivasan; Haunsø, Stig; Burstein, Ethan S.; Whistler, Jennifer L.; Sheikh, Søren P.; Lichtarge, Olivier; Hansen, Jakob Lerche

2010-01-01

Seven transmembrane (7TM) or G protein-coupled receptors constitute a large superfamily of cell surface receptors sharing a structural motif of seven transmembrane spanning alpha helices. Their activation mechanism most likely involves concerted movements of the transmembrane helices, but remains to be completely resolved. Evolutionary Trace (ET) analysis is a computational method, which identifies clusters of functionally important residues by integrating information on evolutionary important residue variations with receptor structure. Combined with known mutational data, ET predicted a patch of residues in the cytoplasmic parts of TM2, TM3, and TM6 to form an activation switch that is common to all family A 7TM receptors. We tested this hypothesis in the rat Angiotensin II (Ang II) type 1 (AT1) receptor. The receptor has important roles in the cardiovascular system, but has also frequently been applied as a model for 7TM receptor activation and signaling. Six mutations: F66A, L67R, L70R, L119R, D125A, and I245F were targeted to the putative switch and assayed for changes in activation state by their ligand binding, signaling, and trafficking properties. All but one receptor mutant (that was not expressed well) displayed phenotypes associated with changed activation state, such as increased agonist affinity or basal activity, promiscuous activation, or constitutive internalization highlighting the importance of testing different signaling pathways. We conclude that this evolutionary important patch mediates interactions important for maintaining the inactive state. More broadly, these observations in the AT1 receptor are consistent with computational predictions of a generic role for this patch in 7TM receptor activation. PMID:20227396

Extruder system and method for treatment of a gaseous medium

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

Silvi, Norberto; Perry, Robert James; Singh, Surinder Prabhjot

A system for treatment of a gaseous medium, comprises an extruder having a barrel. The extruder further comprises a first inlet port, a second inlet port, and a plurality of outlet ports coupled to the barrel. The first inlet port is configured for feeding a lean sorbent, the second inlet port is configured for feeding a gaseous medium, and the plurality of outlet ports are configured for releasing a plurality of components removed from the gaseous medium. Further, the extruder comprises a plurality of helical elements coupled to a plurality of kneading elements, mounted on a shaft, and disposed withinmore » the barrel. The barrel and the plurality of helical and kneading elements together form an absorption unit and a desorption unit. The first and second inlet ports are formed in the absorption unit and the plurality of outlet ports are formed in the absorption and desorption units.« less

High-performance silicon photonic tri-state switch based on balanced nested Mach-Zehnder interferometer.

PubMed

Lu, Zeqin; Celo, Dritan; Mehrvar, Hamid; Bernier, Eric; Chrostowski, Lukas

2017-09-25

This work proposes a novel silicon photonic tri-state (cross/bar/blocking) switch, featuring high-speed switching, broadband operation, and crosstalk-free performance. The switch is designed based on a 2 × 2 balanced nested Mach-Zehnder interferometer structure with carrier injection phase tuning. As compared to silicon photonic dual-state (cross/bar) switches based on Mach-Zehnder interferometers with carrier injection phase tuning, the proposed switch not only has better performance in cross/bar switching but also provides an extra blocking state. The unique blocking state has a great advantage in applications of N × N switch fabrics, where idle switching elements in the fabrics can be configured to the blocking state for crosstalk suppression. According to our numerical experiments on a fully loaded 8 × 8 dilated Banyan switch fabric, the worst output crosstalk of the 8 × 8 switch can be dramatically suppressed by more than 50 dB, by assigning the blocking state to idle switching elements in the fabric. The results of this work can extend the functionality of silicon photonic switches and significantly improve the performance of on-chip N × N photonic switching technologies.

Angular Random Walk Estimation of a Time-Domain Switching Micromachined Gyroscope

DTIC Science & Technology

2016-10-19

1 2. PARAMETRIC SYSTEM IDENTIFICATION BASED ON TIME-DOMAIN SWITCHING ........ 2 3. FINITE ELEMENT MODELING OF RESONATOR...8 3. FINITE ELEMENT MODELING OF RESONATOR This section details basic finite element modeling of the resonator used with the TDSMG. While it...Based on finite element simulations of the employed resonator, it is found that the effects of thermomechanical noise is on par with 10 ps of timing

Cycling firing method for bypass operation of bridge converters

DOEpatents

Zabar, Zivan

1982-01-01

The bridge converter comprises a number of switching elements and an electronic logic system which regulated the electric power levels by controlling the firing, i.e., the initiation of the conduction period of the switching elements. Cyclic firing of said elements allows the direct current to bypass the alternating current system with high power factor and negligible losses.

Advanced gearbox technology

NASA Technical Reports Server (NTRS)

Anderson, N. E.; Cedoz, R. W.; Salama, E. E.; Wagner, D. A.

1987-01-01

An advanced 13,000 HP, counterrotating (CR) gearbox was designed and successfully tested to provide a technology base for future designs of geared propfan propulsion systems for both commercial and military aircraft. The advanced technology CR gearbox was designed for high efficiency, low weight, long life, and improved maintainability. The differential planetary CR gearbox features double helical gears, double row cylindrical roller bearings integral with planet gears, tapered roller prop support bearings, and a flexible ring gear and diaphragm to provide load sharing. A new Allison propfan back-to-back gearbox test facility was constructed. Extensive rotating and stationary instrumentation was used to measure temperature, strain, vibration, deflection and efficiency under representative flight operating conditions. The tests verified smooth, efficient gearbox operation. The highly-instrumented advanced CR gearbox was successfully tested to design speed and power (13,000 HP), and to a 115 percent overspeed condition. Measured CR gearbox efficiency was 99.3 percent at the design point based on heat loss to the oil. Tests demonstrated low vibration characteristics of double helical gearing, proper gear tooth load sharing, low stress levels, and the high load capacity of the prop tapered roller bearings. Applied external prop loads did not significantly affect gearbox temperature, vibration, or stress levels. Gearbox hardware was in excellent condition after the tests with no indication of distress.

Remote Optical Switch for Localized and Selective Control of Gene Interference

PubMed Central

Lee, Somin Eunice; Liu, Gang Logan; Kim, Franklin; Lee, Luke P.

2009-01-01

Near infrared-absorbing gold nanoplasmonic particles (GNPs) are used as optical switches of gene interference and are remotely controlled using light. We have tuned optical switches to a wavelength where cellular photodamage is minimized. Optical switches are functionalized with double-stranded oligonucleotides. At desired times and at specific intracellular locations, remote optical excitation is used to liberate gene-interfering oligonucleotides. We demonstrate a novel gene-interfering technique offering spatial and temporal control, which is otherwise impossible using conventional gene-interfering techniques. PMID:19128006

A double-helix and cross-patterned solenoid used as a wirelessly powered receiver for medical implants

NASA Astrophysics Data System (ADS)

Mao, Shitong; Wang, Hao; Mao, Zhi-Hong; Sun, Mingui

2018-05-01

Many medical implants need to be designed in the shape of a cylinder (rod), a cuboid or a capsule in order to adapt to a specific site within the human body or facilitate the implantation procedure. In order to wirelessly power these types of implants, a pair of coils, one is located inside the human body and one is outside, is often used. Since most organs such as major muscles, blood vessels, and nerve bundles are anatomically parallel to the body surface, the most desired wireless power transfer (WPT) direction is from the external power transmission pad (a planar coil) to the lateral surface of the implant. However, to obtain optimal coupling, the currently used solenoid coil requires being positioned perpendicular to the body surface, which is often medically or anatomically unacceptable. In this research, a concentric double-helix (DH) coil with an air core is presented for use in implantable devices. Two helical coils are tilted at opposite angles (±45 degrees) to form a cross pattern. The WPT system is designed using the magnetic resonance concept for wireless power transfer (MR-WPT). The power transfer efficiency (PTE) relies on the near-field magnetic coupling which is closely related to the location and orientation of the DH coil. We explain how the novel structure of the DH solenoid magnifies the mutual inductance with the widely adopted circular planner coil and how the PTE is improved in comparison to the case of the conventional solenoid coil. We also study an important case where the double-helix power reception coil is laterally and angularly misaligned with the transmitter. Finally, our computational study using the finite element method and experimental study with actually constructed prototypes are presented which have proven our new double-helix coil design.

Tensile properties of helical auxetic structures: A numerical study

NASA Astrophysics Data System (ADS)

Wright, J. R.; Sloan, M. R.; Evans, K. E.

2010-08-01

This paper discusses a helical auxetic structure which has a diverse range of practical applications. The mechanical properties of the system can be determined by particular combinations of geometry and component material properties; finite element analysis is used to investigate the static behavior of these structures under tension. Modeling criteria are determined and design issues are discussed. A description of the different strain-dependent mechanical phases is provided. It is shown that the stiffnesses of the component fibers and the initial helical wrap angle are critical design parameters, and that strain-dependent changes in cross-section must be taken into consideration: we observe that the structures exhibit nonlinear behavior due to nonzero component Poisson's ratios. Negative Poisson's ratios for the helical structures as low as -5 are shown. While we focus here on the structure as a yarn our findings are, in principle, scaleable.

Review: Electrostatically actuated nanobeam-based nanoelectromechanical switches – materials solutions and operational conditions

PubMed Central

Jasulaneca, Liga; Kosmaca, Jelena; Meija, Raimonds; Andzane, Jana

2018-01-01

This review summarizes relevant research in the field of electrostatically actuated nanobeam-based nanoelectromechanical (NEM) switches. The main switch architectures and structural elements are briefly described and compared. Investigation methods that allow for exploring coupled electromechanical interactions as well as studies of mechanically or electrically induced effects are covered. An examination of the complex nanocontact behaviour during various stages of the switching cycle is provided. The choice of the switching element and the electrode is addressed from the materials perspective, detailing the benefits and drawbacks for each. An overview of experimentally demonstrated NEM switching devices is provided, and together with their operational parameters, the reliability issues and impact of the operating environment are discussed. Finally, the most common NEM switch failure modes and the physical mechanisms behind them are reviewed and solutions proposed. PMID:29441272

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.

Illuminated push-button switch

NASA Technical Reports Server (NTRS)

Iwagiri, T.

1983-01-01

An illuminated push-button switch is described. It is characterized by the fact that is consists of a switch group, an operator button opening and closing the switch group, and a light-emitting element which illuminates the face of the operator button.

Solution structure of CEH-37 homeodomain of the nematode Caenorhabditis elegans

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

Moon, Sunjin; Lee, Yong Woo; Kim, Woo Taek

Highlights: •We have determined solution structures of CEH-37 homedomain. •CEH-37 HD has a compact α-helical structure with HTH DNA binding motif. •Solution structure of CEH-37 HD shares its molecular topology with that of the homeodomain proteins. •Residues in the N-terminal region and HTH motif are important in binding to Caenorhabditis elegans telomeric DNA. •CEH-37 could play an important role in telomere function via DNA binding. -- Abstract: The nematode Caenorhabditis elegans protein CEH-37 belongs to the paired OTD/OTX family of homeobox-containing homeodomain proteins. CEH-37 shares sequence similarity with homeodomain proteins, although it specifically binds to double-stranded C. elegans telomeric DNA,more » which is unusual to homeodomain proteins. Here, we report the solution structure of CEH-37 homeodomain and molecular interaction with double-stranded C. elegans telomeric DNA using nuclear magnetic resonance (NMR) spectroscopy. NMR structure shows that CEH-37 homeodomain is composed of a flexible N-terminal region and three α-helices with a helix-turn-helix (HTH) DNA binding motif. Data from size-exclusion chromatography and fluorescence spectroscopy reveal that CEH-37 homeodomain interacts strongly with double-stranded C. elegans telomeric DNA. NMR titration experiments identified residues responsible for specific binding to nematode double-stranded telomeric DNA. These results suggest that C. elegans homeodomain protein, CEH-37 could play an important role in telomere function via DNA binding.« less

47 CFR 69.111 - Tandem-switched transport and tandem charge.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 3 2011-10-01 2011-10-01 false Tandem-switched transport and tandem charge. 69... SERVICES (CONTINUED) ACCESS CHARGES Computation of Charges § 69.111 Tandem-switched transport and tandem...-switched transport shall consist of two rate elements, a transmission charge and a tandem switching charge...

Structural analysis of a class III preQ 1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics

DOE PAGES

Liberman, Joseph A.; Suddala, Krishna C.; Aytenfisu, Asaminew; ...

2015-06-23

PreQ 1-III riboswitches are newly identified RNA elements that control bacterial genes in response to preQ 1 (7-aminomethyl-7-deazaguanine), a precursor to the essential hypermodified tRNA base queuosine. Although numerous riboswitches fold as H-type or HL out-type pseudoknots that integrate ligand-binding and regulatory sequences within a single folded domain, the preQ 1-III riboswitch aptamer forms a HL out-type pseudoknot that does not appear to incorporate its ribosome-binding site (RBS). To understand how this unusual organization confers function, in this paper we determined the crystal structure of the class III preQ 1 riboswitch from Faecalibacterium prausnitzii at 2.75 Å resolution. PreQ 1more » binds tightly (K D,app 6.5 ± 0.5 nM) between helices P1 and P2 of a three-way helical junction wherein the third helix, P4, projects orthogonally from the ligand-binding pocket, exposing its stem-loop to base pair with the 3' RBS. Biochemical analysis, computational modeling, and single-molecule FRET imaging demonstrated that preQ 1 enhances P4 reorientation toward P1–P2, promoting a partially nested, H-type pseudoknot in which the RBS undergoes rapid docking (k dock ~0.6 s -1) and undocking (k undock ~1.1 s -1). Finally, discovery of such dynamic conformational switching provides insight into how a riboswitch with bipartite architecture uses dynamics to modulate expression platform accessibility, thus expanding the known repertoire of gene control strategies used by regulatory RNAs.« less

High-Power X-Band Semiconductor RF Switch for Pulse Compression Systems of Future Colliders

NASA Astrophysics Data System (ADS)

Tantawi, Sami G.; Tamura, Fumihiko

2000-04-01

We describe the potential of semiconductor X-band RF switch arrays as a means of developing high power RF pulse compression systems for future linear colliders. The switch systems described here have two designs. Both designs consist of two 3dB hybrids and active modules. In the first design the module is composed of a cascaded active phase shifter. In the second design the module uses arrays of SPST (Single Pole Single Throw) switches. Each cascaded element of the phase shifter and the SPST switch has similar design. The active element consists of symmetrical three-port tee-junctions and an active waveguide window in the symmetrical arm of the tee-junction. The design methodology of the elements and the architecture of the whole switch system are presented. We describe the scaling law that governs the relation between power handling capability and number of elements. The design of the active waveguide window is presented. The waveguide window is a silicon wafer with an array of four hundred PIN/NIP diodes covering the surface of the window. This waveguide window is located in an over-moded TE01 circular waveguide. The results of high power RF measurements of the active waveguide window are presented. The experiment is performed at power levels of tens of megawatts at X-band.

Super Nonlinear Electrodeposition-Diffusion-Controlled Thin-Film Selector.

PubMed

Ji, Xinglong; Song, Li; He, Wei; Huang, Kejie; Yan, Zhiyuan; Zhong, Shuai; Zhang, Yishu; Zhao, Rong

2018-03-28

Selector elements with high nonlinearity are an indispensable part in constructing high density, large-scale, 3D stackable emerging nonvolatile memory and neuromorphic network. Although significant efforts have been devoted to developing novel thin-film selectors, it remains a great challenge in achieving good switching performance in the selectors to satisfy the stringent electrical criteria of diverse memory elements. In this work, we utilized high-defect-density chalcogenide glass (Ge 2 Sb 2 Te 5 ) in conjunction with high mobility Ag element (Ag-GST) to achieve a super nonlinear selective switching. A novel electrodeposition-diffusion dynamic selector based on Ag-GST exhibits superior selecting performance including excellent nonlinearity (<5 mV/dev), ultra-low leakage (<10 fA), and bidirectional operation. With the solid microstructure evidence and dynamic analyses, we attributed the selective switching to the competition between the electrodeposition and diffusion of Ag atoms in the glassy GST matrix under electric field. A switching model is proposed, and the in-depth understanding of the selective switching mechanism offers an insight of switching dynamics for the electrodeposition-diffusion-controlled thin-film selector. This work opens a new direction of selector designs by combining high mobility elements and high-defect-density chalcogenide glasses, which can be extended to other materials with similar properties.

Conformational equilibria of light-activated rhodopsin in nanodiscs

PubMed Central

Van Eps, Ned; Caro, Lydia N.; Morizumi, Takefumi; Kusnetzow, Ana Karin; Szczepek, Michal; Hofmann, Klaus Peter; Bayburt, Timothy H.; Sligar, Stephen G.; Ernst, Oliver P.; Hubbell, Wayne L.

2017-01-01

Conformational equilibria of G-protein–coupled receptors (GPCRs) are intimately involved in intracellular signaling. Here conformational substates of the GPCR rhodopsin are investigated in micelles of dodecyl maltoside (DDM) and in phospholipid nanodiscs by monitoring the spatial positions of transmembrane helices 6 and 7 at the cytoplasmic surface using site-directed spin labeling and double electron–electron resonance spectroscopy. The photoactivated receptor in DDM is dominated by one conformation with weak pH dependence. In nanodiscs, however, an ensemble of pH-dependent conformational substates is observed, even at pH 6.0 where the MIIbH+ form defined by proton uptake and optical spectroscopic methods is reported to be the sole species present in native disk membranes. In nanodiscs, the ensemble of substates in the photoactivated receptor spontaneously decays to that characteristic of the inactive state with a lifetime of ∼16 min at 20 °C. Importantly, transducin binding to the activated receptor selects a subset of the ensemble in which multiple substates are apparently retained. The results indicate that in a native-like lipid environment rhodopsin activation is not analogous to a simple binary switch between two defined conformations, but the activated receptor is in equilibrium between multiple conformers that in principle could recognize different binding partners. PMID:28373559

Membrane-spanning α-helical barrels as tractable protein-design targets.

PubMed

Niitsu, Ai; Heal, Jack W; Fauland, Kerstin; Thomson, Andrew R; Woolfson, Derek N

2017-08-05

The rational ( de novo ) design of membrane-spanning proteins lags behind that for water-soluble globular proteins. This is due to gaps in our knowledge of membrane-protein structure, and experimental difficulties in studying such proteins compared to water-soluble counterparts. One limiting factor is the small number of experimentally determined three-dimensional structures for transmembrane proteins. By contrast, many tens of thousands of globular protein structures provide a rich source of 'scaffolds' for protein design, and the means to garner sequence-to-structure relationships to guide the design process. The α-helical coiled coil is a protein-structure element found in both globular and membrane proteins, where it cements a variety of helix-helix interactions and helical bundles. Our deep understanding of coiled coils has enabled a large number of successful de novo designs. For one class, the α-helical barrels-that is, symmetric bundles of five or more helices with central accessible channels-there are both water-soluble and membrane-spanning examples. Recent computational designs of water-soluble α-helical barrels with five to seven helices have advanced the design field considerably. Here we identify and classify analogous and more complicated membrane-spanning α-helical barrels from the Protein Data Bank. These provide tantalizing but tractable targets for protein engineering and de novo protein design.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'. © 2017 The Author(s).

Polarized excitons and optical activity in single-wall carbon nanotubes

NASA Astrophysics Data System (ADS)

Chang, Yao-Wen; Jin, Bih-Yaw

2018-05-01

The polarized excitons and optical activity of single-wall carbon nanotubes (SWNTs) are studied theoretically by π -electron Hamiltonian and helical-rotational symmetry. By taking advantage of the symmetrization, the single-particle energy and properties of a SWNT are characterized with the corresponding helical band structure. The dipole-moment matrix elements, magnetic-moment matrix elements, and the selection rules can also be derived. Based on different selection rules, the optical transitions can be assigned as the parallel-polarized, left-handed circularly-polarized, and right-handed circularly-polarized transitions, where the combination of the last two gives the cross-polarized transition. The absorption and circular dichroism (CD) spectra are simulated by exciton calculation. The calculated results are well comparable with the reported measurements. Built on the foundation, magnetic-field effects on the polarized excitons and optical activity of SWNTs are studied. Dark-bright exciton splitting and interband Faraday effect in the CD spectrum of SWNTs under an axial magnetic field are predicted. The Faraday rotation dispersion can be analyzed according to the selection rules of circular polarizations and the helical band structure.

Off-shell amplitudes as boundary integrals of analytically continued Wilson line slope

NASA Astrophysics Data System (ADS)

Kotko, P.; Serino, M.; Stasto, A. M.

2016-08-01

One of the methods to calculate tree-level multi-gluon scattering amplitudes is to use the Berends-Giele recursion relation involving off-shell currents or off-shell amplitudes, if working in the light cone gauge. As shown in recent works using the light-front perturbation theory, solutions to these recursions naturally collapse into gauge invariant and gauge-dependent components, at least for some helicity configurations. In this work, we show that such structure is helicity independent and emerges from analytic properties of matrix elements of Wilson line operators, where the slope of the straight gauge path is shifted in a certain complex direction. This is similar to the procedure leading to the Britto-Cachazo-Feng-Witten (BCFW) recursion, however we apply a complex shift to the Wilson line slope instead of the external momenta. While in the original BCFW procedure the boundary integrals over the complex shift vanish for certain deformations, here they are non-zero and are equal to the off-shell amplitudes. The main result can thus be summarized as follows: we derive a decomposition of a helicity-fixed off-shell current into gauge invariant component given by a matrix element of a straight Wilson line plus a reminder given by a sum of products of gauge invariant and gauge dependent quantities. We give several examples realizing this relation, including the five-point next-to-MHV helicity configuration.

A Mutation Directs the Structural Switch of DNA Binding Proteins under Starvation to a Ferritin-like Protein Cage.

PubMed

Williams, Sunanda Margrett; Chandran, Anu Vijayakumari; Prakash, Sunita; Vijayan, Mamannamana; Chatterji, Dipankar

2017-09-05

Proteins of the ferritin family are ubiquitous in living organisms. With their spherical cage-like structures they are the iron storehouses in cells. Subfamilies of ferritins include 24-meric ferritins and bacterioferritins (maxiferritins), and 12-meric Dps (miniferritins). Dps safeguards DNA by direct binding, affording physical protection and safeguards from free radical-mediated damage by sequestering iron in its core. The maxiferritins can oxidize and store iron but cannot bind DNA. Here we show that a mutation at a critical interface in Dps alters its assembly from the canonical 12-mer to a ferritin-like 24-mer under crystallization. This structural switch was attributed to the conformational alteration of a highly conserved helical loop and rearrangement of the C-terminus. Our results demonstrate a novel concept of mutational switch between related protein subfamilies and corroborate the popular model for evolution by which subtle substitutions in an amino acid sequence lead to diversification among proteins. Copyright © 2017 Elsevier Ltd. All rights reserved.

NMR structure of the DNA decamer duplex containing double T*G mismatches of cis-syn cyclobutane pyrimidine dimer: implications for DNA damage recognition by the XPC-hHR23B complex.

PubMed

Lee, Joon-Hwa; Park, Chin-Ju; Shin, Jae-Sun; Ikegami, Takahisa; Akutsu, Hideo; Choi, Byong-Seok

2004-01-01

The cis-syn cyclobutane pyrimidine dimer (CPD) is a cytotoxic, mutagenic and carcinogenic DNA photoproduct and is repaired by the nucleotide excision repair (NER) pathway in mammalian cells. The XPC-hHR23B complex as the initiator of global genomic NER binds to sites of certain kinds of DNA damage. Although CPDs are rarely recognized by the XPC-hHR23B complex, the presence of mismatched bases opposite a CPD significantly increased the binding affinity of the XPC-hHR23B complex to the CPD. In order to decipher the properties of the DNA structures that determine the binding affinity for XPC-hHR23B to DNA, we carried out structural analyses of the various types of CPDs by NMR spectroscopy. The DNA duplex which contains a single 3' T*G wobble pair in a CPD (CPD/GA duplex) induces little conformational distortion. However, severe distortion of the helical conformation occurs when a CPD contains double T*G wobble pairs (CPD/GG duplex) even though the T residues of the CPD form stable hydrogen bonds with the opposite G residues. The helical bending angle of the CPD/GG duplex was larger than those of the CPD/GA duplex and properly matched CPD/AA duplex. The fluctuation of the backbone conformation and significant changes in the widths of the major and minor grooves at the double T*G wobble paired site were also observed in the CPD/GG duplex. These structural features were also found in a duplex that contains the (6-4) adduct, which is efficiently recognized by the XPC-hHR23B complex. Thus, we suggest that the unique structural features of the DNA double helix (that is, helical bending, flexible backbone conformation, and significant changes of the major and/or minor grooves) might be important factors in determining the binding affinity of the XPC-hHR23B complex to DNA.

MinD-dependent conformational changes in MinE required for the Min oscillator to spatially regulate cytokinesis

PubMed Central

Park, Kyung-Tae; Wu, Wei; Battaile, Kevin P.; Lovell, Scott; Holyoak, Todd; Lutkenhaus, Joe

2011-01-01

Summary MinD recruits MinE to the membrane leading to a coupled oscillation required for spatial regulation of the cytokinetic Z ring in E. coli. How these proteins interact, however, is not clear since the MinD binding regions of MinE are sequestered within a 6-stranded β-sheet and masked by N-terminal helices. Here, minE mutations are isolated that restore interaction to some MinD and MinE mutants. These mutations alter the MinE structure releasing the MinD binding regions and N-terminal helices that bind MinD and the membrane, respectively. Crystallization of MinD-MinE complexes reveals a 4-stranded β-sheet MinE dimer with the released β strands (MinD binding regions) converted to α-helices bound to MinD dimers. These results suggest a 6 stranded, β-sheet dimer of MinE ‘senses’ MinD and switches to a 4-stranded β-sheet dimer that binds MinD and contributes to membrane binding. Also, the results indicate how MinE persists at the MinD-membrane surface. PMID:21816275

Solution structure of the antitermination protein NusB of Escherichia coli: a novel all-helical fold for an RNA-binding protein.

PubMed Central

Huenges, M; Rölz, C; Gschwind, R; Peteranderl, R; Berglechner, F; Richter, G; Bacher, A; Kessler, H; Gemmecker, G

1998-01-01

The NusB protein of Escherichia coli is involved in the regulation of rRNA biosynthesis by transcriptional antitermination. In cooperation with several other proteins, it binds to a dodecamer motif designated rrn boxA on the nascent rRNA. The antitermination proteins of E.coli are recruited in the replication cycle of bacteriophage lambda, where they play an important role in switching from the lysogenic to the lytic cycle. Multidimensional heteronuclear NMR experiments were performed with recombinant NusB protein labelled with 13C, 15N and 2H. The three-dimensional structure of the protein was solved from 1926 NMR-derived distances and 80 torsion angle restraints. The protein folds into an alpha/alpha-helical topology consisting of six helices; the arginine-rich N-terminus appears to be disordered. Complexation of the protein with an RNA dodecamer equivalent to the rrn boxA site results in chemical shift changes of numerous amide signals. The overall packing of the protein appears to be conserved, but the flexible N-terminus adopts a more rigid structure upon RNA binding, indicating that the N-terminus functions as an arginine-rich RNA-binding motif (ARM). PMID:9670024

Circulating current battery heater

DOEpatents

Ashtiani, Cyrus N.; Stuart, Thomas A.

2001-01-01

A circuit for heating energy storage devices such as batteries is provided. The circuit includes a pair of switches connected in a half-bridge configuration. Unidirectional current conduction devices are connected in parallel with each switch. A series resonant element for storing energy is connected from the energy storage device to the pair of switches. An energy storage device for intermediate storage of energy is connected in a loop with the series resonant element and one of the switches. The energy storage device which is being heated is connected in a loop with the series resonant element and the other switch. Energy from the heated energy storage device is transferred to the switched network and then recirculated back to the battery. The flow of energy through the battery causes internal power dissipation due to electrical to chemical conversion inefficiencies. The dissipated power causes the internal temperature of the battery to increase. Higher internal temperatures expand the cold temperature operating range and energy capacity utilization of the battery. As disclosed, either fixed frequency or variable frequency modulation schemes may be used to control the network.

Effects of doping concentration ratio on electrical characterization in pseudomorphic HEMT-based MMIC switches for ICT system

NASA Astrophysics Data System (ADS)

Mun, Jae-Kyoung; Oh, Jung-Hun; Sung, Ho-Kun; Wang, Cong

2015-12-01

The effects of the doping concentration ratios between upper and lower silicon planar-doping layers on the DC and RF characteristics of the double planar doped pseudomorphic high electron mobility transistors (pHEMTs) are investigated. From the device simulation, an increase of maximum extrinsic transconductance and a decrease of total on- and off-state capacitances are observed, as well as an increase of the upper to lower planar-doping concentration ratios (UTLPDR), which give rise to an enhancement of the switching speed and isolation characteristics. On the basis of simulation results, two types of pHEMTs are fabricated with two different UTLPDRs of 4:1 and 1:2. After applying these two types' pHEMTs, single-pole-double-throw (SPDT) transmitter/receiver monolithic microwave integrated circuit (MMIC) switches are also designed and fabricated. The SPDT MMIC switch with a 4:1 UTLPDR shows an insertion loss of 0.58 dB, isolation of 40.2 dB, and switching speed of 100 ns, respectively, which correspondingly indicate a 0.23 dB lower insertion loss, 2.90 dB higher isolation and 2.5 times faster switching speed than those of 1:2 UTLPDR at frequency range of 2-6 GHz. From the simulation results and comparative studies, we propose that the UTLPDR must be greater than 4:1 for the best switching performance. With the abovementioned excellent performances, the proposed switch would be quite promising in the application of information and communications technology system.

X-ray diffraction from nonuniformly stretched helical molecules

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

Prodanovic, Momcilo; Irving, Thomas C.; Mijailovich, Srboljub M.

2016-04-18

The fibrous proteins in living cells are exposed to mechanical forces interacting with other subcellular structures. X-ray fiber diffraction is often used to assess deformation and movement of these proteins, but the analysis has been limited to the theory for fibrous molecular systems that exhibit helical symmetry. However, this approach cannot adequately interpret X-ray data from fibrous protein assemblies where the local strain varies along the fiber length owing to interactions of its molecular constituents with their binding partners. To resolve this problem a theoretical formulism has been developed for predicting the diffraction from individual helical molecular structures nonuniformly strainedmore » along their lengths. This represents a critical first step towards modeling complex dynamical systems consisting of multiple helical structures using spatially explicit, multi-scale Monte Carlo simulations where predictions are compared with experimental data in a `forward' process to iteratively generate ever more realistic models. Here the effects of nonuniform strains and the helix length on the resulting magnitude and phase of diffraction patterns are quantitatively assessed. Examples of the predicted diffraction patterns of nonuniformly deformed double-stranded DNA and actin filaments in contracting muscle are presented to demonstrate the feasibly of this theoretical approach.« less

Double Q-switch Ho:Sc2SiO5 laser by acousto-optic modulator combined with Cr2+:ZnSe saturable absorber

NASA Astrophysics Data System (ADS)

Yang, Xiao-tao; Zhang, Peng; Xie, Wen-qiang; Li, Lin-jun

2018-01-01

A double Q-switch (DQS) Ho:Sc2SiO5 laser modulated by a acousto-optic modulators (AOM) combined with a Cr2+:ZnSe saturable absorber (SA) was reported for the first time. The actively Q-switch (AQS) and passively Q-switch (PQS) were also studied. For the DQS mode, a maximum average output power of 2.49 W under the incident pump power of 12.5 W was obtained, corresponding to a slope efficiency of 24%. The characteristics of the DQS Ho:SSO laser versus different repetition frequencies (RF) of the AOM were researched. The maximum single-pulse energy of the DQS Ho:SSO laser was calculated to 1.98 mJ. The maximum peak power of the DQS Ho:SSO laser was 49.5 kW. The output beam quality factor M2 of DQS Ho:SSO laser was measured to be 1.15 with the highest peak power by knife-edge method at different positions.

Band edge tailoring of InGaAs/AlAsSb coupled double quantum wells for a monolithically integrated all-optical switch.

PubMed

Feng, Jijun; Akimoto, Ryoichi; Gozu, Shin-ichiro; Mozume, Teruo; Hasama, Toshifumi; Ishikawa, Hiroshi

2013-07-01

We demonstrate a compact all-optical Michelson interferometer (MI) gating switch with monolithic integration of two different bandgap energies. Based on the ion-induced intermixing in InGaAs/AlAsSb coupled double quantum wells, the blueshift of the band edge can be tailored. Through phosphorus ion implantation with a dose of 5 × 10(14) cm(-2) and subsequent annealing at 720 °C for 60 s, an implanted sample can acquire a high transmittance compared with the as-grown one. Meanwhile, the cross-phase modulation (XPM) efficiency of a non-implanted sample undergoing the same annealing process decreases little. An implanted part for signal propagation and a non-implanted section for XPM are thus monolithically integrated for an MI switch by an area-selective manner. Full switching of a π-rad nonlinear phase shift is achieved with pump pulse energy of 5.6 pJ at a 10-GHz repetition rate.

Effect of platform switching on the peri-implant bone: A finite element study

PubMed Central

Martínez-González, Amparo; Peiró, Germán; Ródenas, Juan-José; López-Mollá, María-Victoria

2015-01-01

Background There exists a relation between the presence and location of the micro-gap and the loss of peri implant bone. Several authors have shown that the treatments based on the use of platform switching result in less peri-implant bone loss and an increased tissue stability. The purpose of this study was to analyse the effect of the platform switching on the distribution of stresses on the peri-implant bone using the finite element method. Material and Methods A realistic 3D full-mandible finite element model representing cortical bone and trabecular bone was used to study the distribution of the stress on the bone induced by an implant of diameter 4.1 mm. Two abutments were modelled. The first one, of diameter 4.1 mm, was used in the reference model to represent a conventional implant. The second one, of diameter 3.2 mm, was used to represent the implant with platform switching. Both models were subjected to axial and oblique masticatory loads. Results The analyses showed that, although no relevant differences can be found for the trabecular bone, the use of platform switching reduces the maximum stress level in the cortical bone by almost 36% with axial loads and by 40% with oblique loads. Conclusions The full 3D Finite Element model, that can be used to investigate the influence of other parameters (implant diameter, connexion type, …) on the biomechanical behaviour of the implant, showed that this stress reduction can be a biomechanical reasons to explain why the platform switching seems to reduce or eliminate crestal bone resorption after the prosthetic restoration. Key words:Dental implant, platform switching, finite element method. PMID:26535094

Vestigialization of an Allosteric Switch: Genetic and Structural Mechanisms for the Evolution of Constitutive Activity in a Steroid Hormone Receptor

PubMed Central

Bridgham, Jamie T.; Keay, June; Ortlund, Eric A.; Thornton, Joseph W.

2014-01-01

An important goal in molecular evolution is to understand the genetic and physical mechanisms by which protein functions evolve and, in turn, to characterize how a protein's physical architecture influences its evolution. Here we dissect the mechanisms for an evolutionary shift in function in the mollusk ortholog of the steroid hormone receptors (SRs), a family of biologically essential transcription factors. In vertebrates, the activity of SRs allosterically depends on binding a hormonal ligand; in mollusks, however, the SR ortholog (called ER, because of high sequence similarity to vertebrate estrogen receptors) activates transcription in the absence of ligand and does not respond to steroid hormones. To understand how this shift in regulation evolved, we combined evolutionary, structural, and functional analyses. We first determined the X-ray crystal structure of the ER of the Pacific oyster Crassostrea gigas (CgER), and found that its ligand pocket is filled with bulky residues that prevent ligand occupancy. To understand the genetic basis for the evolution of mollusk ERs' unique functions, we resurrected an ancient SR progenitor and characterized the effect of historical amino acid replacements on its functions. We found that reintroducing just two ancient replacements from the lineage leading to mollusk ERs recapitulates the evolution of full constitutive activity and the loss of ligand activation. These substitutions stabilize interactions among key helices, causing the allosteric switch to become “stuck” in the active conformation and making activation independent of ligand binding. Subsequent changes filled the ligand pocket without further affecting activity; by degrading the allosteric switch, these substitutions vestigialized elements of the protein's architecture required for ligand regulation and made reversal to the ancestral function more complex. These findings show how the physical architecture of allostery enabled a few large-effect mutations to trigger a profound evolutionary change in the protein's function and shaped the genetics of evolutionary reversibility. PMID:24415950

Staufen1 senses overall transcript secondary structure to regulate translation

PubMed Central

Ricci, Emiliano P; Kucukural, Alper; Cenik, Can; Mercier, Blandine C; Singh, Guramrit; Heyer, Erin E; Ashar-Patel, Ami; Peng, Lingtao; Moore, Melissa J

2015-01-01

Human Staufen1 (Stau1) is a double-stranded RNA (dsRNA)-binding protein implicated in multiple post-transcriptional gene-regulatory processes. Here we combined RNA immunoprecipitation in tandem (RIPiT) with RNase footprinting, formaldehyde cross-linking, sonication-mediated RNA fragmentation and deep sequencing to map Staufen1-binding sites transcriptome wide. We find that Stau1 binds complex secondary structures containing multiple short helices, many of which are formed by inverted Alu elements in annotated 3′ untranslated regions (UTRs) or in ‘strongly distal’ 3′ UTRs. Stau1 also interacts with actively translating ribosomes and with mRNA coding sequences (CDSs) and 3′ UTRs in proportion to their GC content and propensity to form internal secondary structure. On mRNAs with high CDS GC content, higher Stau1 levels lead to greater ribosome densities, thus suggesting a general role for Stau1 in modulating translation elongation through structured CDS regions. Our results also indicate that Stau1 regulates translation of transcription-regulatory proteins. PMID:24336223

Complementary resistive switching in BaTiO3/NiO bilayer with opposite switching polarities

NASA Astrophysics Data System (ADS)

Li, Shuo; Wei, Xianhua; Lei, Yao; Yuan, Xincai; Zeng, Huizhong

2016-12-01

Resistive switching behaviors have been investigated in the Au/BaTiO3/NiO/Pt structure by stacking the two elements with different switching types. The conducting atomic force microscope measurements on BaTiO3 thin films and NiO thin films suggest that with the same active resistive switching region, the switching polarities in the two semiconductors are opposite to each other. It is in agreement with the bipolar hysteresis I-V curves with opposite switching polarities for single-layer devices. The bilayer devices show complementary resistive switching (CRS) without electroforming and unipolar resistive switching (URS) after electroforming. The coexistence of CRS and URS is mainly ascribed to the co-effect of electric field and Joule heating mechanisms, indicating that changeable of resistance in this device is dominated by the redistribution of oxygen vacancies in BaTiO3 and the formation, disruption, restoration of conducting filaments in NiO. CRS in bilayer with opposite switching polarities is effective to solve the sneak current without the introduction of any selector elements or an additional metal electrode.

Investigation of Dielectric Breakdown Characteristics for Double-break Vacuum Interrupter and Dielectric Breakdown Probability Distribution in Vacuum Interrupter

NASA Astrophysics Data System (ADS)

Shioiri, Tetsu; Asari, Naoki; Sato, Junichi; Sasage, Kosuke; Yokokura, Kunio; Homma, Mitsutaka; Suzuki, Katsumi

To investigate the reliability of equipment of vacuum insulation, a study was carried out to clarify breakdown probability distributions in vacuum gap. Further, a double-break vacuum circuit breaker was investigated for breakdown probability distribution. The test results show that the breakdown probability distribution of the vacuum gap can be represented by a Weibull distribution using a location parameter, which shows the voltage that permits a zero breakdown probability. The location parameter obtained from Weibull plot depends on electrode area. The shape parameter obtained from Weibull plot of vacuum gap was 10∼14, and is constant irrespective non-uniform field factor. The breakdown probability distribution after no-load switching can be represented by Weibull distribution using a location parameter. The shape parameter after no-load switching was 6∼8.5, and is constant, irrespective of gap length. This indicates that the scatter of breakdown voltage was increased by no-load switching. If the vacuum circuit breaker uses a double break, breakdown probability at low voltage becomes lower than single-break probability. Although potential distribution is a concern in the double-break vacuum cuicuit breaker, its insulation reliability is better than that of the single-break vacuum interrupter even if the bias of the vacuum interrupter's sharing voltage is taken into account.

The carboxy-terminal αN helix of the archaeal XerA tyrosine recombinase is a molecular switch to control site-specific recombination.

PubMed

Serre, Marie-Claude; El Arnaout, Toufic; Brooks, Mark A; Durand, Dominique; Lisboa, Johnny; Lazar, Noureddine; Raynal, Bertrand; van Tilbeurgh, Herman; Quevillon-Cheruel, Sophie

2013-01-01

Tyrosine recombinases are conserved in the three kingdoms of life. Here we present the first crystal structure of a full-length archaeal tyrosine recombinase, XerA from Pyrococcus abyssi, at 3.0 Å resolution. In the absence of DNA substrate XerA crystallizes as a dimer where each monomer displays a tertiary structure similar to that of DNA-bound Tyr-recombinases. Active sites are assembled in the absence of dif except for the catalytic Tyr, which is extruded and located equidistant from each active site within the dimer. Using XerA active site mutants we demonstrate that XerA follows the classical cis-cleavage reaction, suggesting rearrangements of the C-terminal domain upon DNA binding. Surprisingly, XerA C-terminal αN helices dock in cis in a groove that, in bacterial tyrosine recombinases, accommodates in trans αN helices of neighbour monomers in the Holliday junction intermediates. Deletion of the XerA C-terminal αN helix does not impair cleavage of suicide substrates but prevents recombination catalysis. We propose that the enzymatic cycle of XerA involves the switch of the αN helix from cis to trans packing, leading to (i) repositioning of the catalytic Tyr in the active site in cis and (ii) dimer stabilisation via αN contacts in trans between monomers.

Programmable resistive-switch nanowire transistor logic circuits.

PubMed

Shim, Wooyoung; Yao, Jun; Lieber, Charles M

2014-09-10

Programmable logic arrays (PLA) constitute a promising architecture for developing increasingly complex and functional circuits through nanocomputers from nanoscale building blocks. Here we report a novel one-dimensional PLA element that incorporates resistive switch gate structures on a semiconductor nanowire and show that multiple elements can be integrated to realize functional PLAs. In our PLA element, the gate coupling to the nanowire transistor can be modulated by the memory state of the resistive switch to yield programmable active (transistor) or inactive (resistor) states within a well-defined logic window. Multiple PLA nanowire elements were integrated and programmed to yield a working 2-to-4 demultiplexer with long-term retention. The well-defined, controllable logic window and long-term retention of our new one-dimensional PLA element provide a promising route for building increasingly complex circuits with nanoscale building blocks.

Generation of spiral optical beams using a spatial light modulator

NASA Astrophysics Data System (ADS)

Rodrigo, Peter J.; Alonzo, Carlo A.; Gluckstad, Jesper

2005-08-01

Recently, a new type of beam termed "spiral optical beam" has been introduced [Alonzo, et al., Opt. Express 13, 1749 (2005)]. Spiral beams are created from multiplicative mixtures of helical and conical phase distributions. Helico-conical phase fronts that generate these novel beams are not achieved with a sequence of a corkscrew wave-plate and an axicon (as this sequence gives a sum of helical and conical phase terms). Nevertheless, the availability of phase-only spatial light modulators (SLM) allows one to directly imprint helico-conical phase functions on an incident plane wave and provides an easy way to modify the profile of the encoded phase. Focusing the phase-modified field results in spiral intensity distributions that may find use for optical manipulation of mesoscopic particles. In this paper, we have extended the discussion to translation and rotation (as well as chirality switching) of the spiral beams using SLM control.

Helicity-dependent cross sections and double-polarization observable E in η photoproduction from quasifree protons and neutrons

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

Witthauer, L.; Dieterle, M.; Abt, S.

2017-05-01

Precise helicity-dependent cross sections and the double-polarization observable E were measured for η photoproduction from quasifree protons and neutrons bound in the deuteron. The η → 2γ and η → 3π 0 → 6γ decay modes were used to optimize the statistical quality of the data and to estimate systematic uncertainties. The measurement used the A2 detector setup at the tagged photon beam of the electron accelerator MAMI in Mainz. A longitudinally polarized deuterated butanol target was used in combination with a circularly polarized photon beam from bremsstrahlung of a longitudinally polarized electron beam. The reaction products were detected withmore » the electromagnetic calorimeters Crystal Ball and TAPS, which covered 98% of the full solid angle. The results show that the narrow structure observed earlier in the unpolarized excitation function of η photoproduction off the neutron appears only in reactions with antiparallel photon and nucleon spin (σ 1/2). It is absent for reactions with parallel spin orientation (σ 3/2) and thus very probably related to partial waves with total spin 1/2. The behavior of the angular distributions of the helicity-dependent cross sections was analyzed by fitting them with Legendre polynomials. The results are in good agreement with a model from the Bonn-Gatchina group, which uses an interference of P 11 and S 11 partial waves to explain the narrow structure.« less

Double charmonia production in exclusive Z-boson decays

NASA Astrophysics Data System (ADS)

Likhoded, A. K.; Luchinsky, A. V.

2018-05-01

This paper is devoted to systematic analysis of double charmonium production in exclusive Z-boson decays in the framework of non-relativistic quantum chromodynamics (NRQCD) and leading twist light-cone (LC) models. Theoretical predictions for branching fractions of all considered decays are presented. According to the obtained results in the case of the allowed helicity suppression rule processes, the effect of internal quark motion increases the branching fractions by a factor 1.5, while for forbidden reactions the LC predictions are strictly zero, while NRQCD ones are significantly smaller than for allowed.

47 CFR 69.404 - Telephone operator services expenses in Account 6620.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 6620. 69.404 Section 69.404 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON... category, and the Local Switching and Information elements based on the relative number of weighted... Switching and Information elements on the basis of the bill rendered for the services provided. ...

Double line groups: structure, irreducible representations and spin splitting of the bands

NASA Astrophysics Data System (ADS)

Lazić, N.; Milivojević, M.; Vuković, T.; Damnjanović, M.

2018-06-01

Double line groups are derived, structurally examined and classified within 13 infinite families. Their irreducible representations, found and tabulated, single out the complete set of conserved quantum numbers in fermionic quasi-one-dimensional systems possessing either translational periodicity or incommensurate helical symmetry. Spin–orbit interaction is analyzed: the induced orbital band splitting and the consequent removal of the spin degeneracy are completely explained. Being incompatible with vertical mirror symmetry, as well as with simultaneous invariance under time-reversal and horizontal (roto)reflections, spin splitting and spin polarized currents may occur only in the systems with the first and the fifth family double line group symmetry. The effects are illustrated on carbon nanotubes.

The beginning of kinesin's force-generating cycle visualized at 9-Å resolution

PubMed Central

Sindelar, Charles V.; Downing, Kenneth H.

2007-01-01

We have used cryo-electron microscopy of kinesin-decorated microtubules to resolve the structure of the motor protein kinesin's crucial nucleotide response elements, switch I and the switch II helix, in kinesin's poorly understood nucleotide-free state. Both of the switch elements undergo conformational change relative to the microtubule-free state. The changes in switch I suggest a role for it in “ejecting” adenosine diphosphate when kinesin initially binds to the microtubule. The switch II helix has an N-terminal extension, apparently stabilized by conserved microtubule contacts, implying a microtubule activation mechanism that could convey the state of the bound nucleotide to kinesin's putative force-delivering element (the “neck linker”). In deriving this structure, we have adapted an image-processing technique, single-particle reconstruction, for analyzing decorated microtubules. The resulting reconstruction visualizes the asymmetric seam present in native, 13-protofilament microtubules, and this method will provide an avenue to higher-resolution characterization of a variety of microtubule- binding proteins, as well as the microtubule itself. PMID:17470637

Flow-induced vibration analysis of a helical coil steam generator experiment using large eddy simulation

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

Yuan, Haomin; Solberg, Jerome; Merzari, Elia

This paper describes a numerical study of flow-induced vibration in a helical coil steam generator experiment conducted at Argonne National Laboratory in the 1980s. In the experiment, a half-scale sector model of a steam generator helical coil tube bank was subjected to still and flowing air and water, and the vibrational characteristics were recorded. The research detailed in this document utilizes the multi-physics simulation toolkit SHARP developed at Argonne National Laboratory, in cooperation with Lawrence Livermore National Laboratory, to simulate the experiment. SHARP uses the spectral element code Nek5000 for fluid dynamics analysis and the finite element code DIABLO formore » structural analysis. The flow around the coil tubes is modeled in Nek5000 by using a large eddy simulation turbulence model. Transient pressure data on the tube surfaces is sampled and transferred to DIABLO for the structural simulation. The structural response is simulated in DIABLO via an implicit time-marching algorithm and a combination of continuum elements and structural shells. Tube vibration data (acceleration and frequency) are sampled and compared with the experimental data. Currently, only one-way coupling is used, which means that pressure loads from the fluid simulation are transferred to the structural simulation but the resulting structural displacements are not fed back to the fluid simulation« less

Flow-induced vibration analysis of a helical coil steam generator experiment using large eddy simulation

DOE PAGES

Yuan, Haomin; Solberg, Jerome; Merzari, Elia; ...

2017-08-01

This study describes a numerical study of flow-induced vibration in a helical coil steam generator experiment conducted at Argonne National Laboratory in the 1980 s. In the experiment, a half-scale sector model of a steam generator helical coil tube bank was subjected to still and flowing air and water, and the vibrational characteristics were recorded. The research detailed in this document utilizes the multi-physics simulation toolkit SHARP developed at Argonne National Laboratory, in cooperation with Lawrence Livermore National Laboratory, to simulate the experiment. SHARP uses the spectral element code Nek5000 for fluid dynamics analysis and the finite element code DIABLOmore » for structural analysis. The flow around the coil tubes is modeled in Nek5000 by using a large eddy simulation turbulence model. Transient pressure data on the tube surfaces is sampled and transferred to DIABLO for the structural simulation. The structural response is simulated in DIABLO via an implicit time-marching algorithm and a combination of continuum elements and structural shells. Tube vibration data (acceleration and frequency) are sampled and compared with the experimental data. Currently, only one-way coupling is used, which means that pressure loads from the fluid simulation are transferred to the structural simulation but the resulting structural displacements are not fed back to the fluid simulation.« less

Flow-induced vibration analysis of a helical coil steam generator experiment using large eddy simulation

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

Yuan, Haomin; Solberg, Jerome; Merzari, Elia

This study describes a numerical study of flow-induced vibration in a helical coil steam generator experiment conducted at Argonne National Laboratory in the 1980 s. In the experiment, a half-scale sector model of a steam generator helical coil tube bank was subjected to still and flowing air and water, and the vibrational characteristics were recorded. The research detailed in this document utilizes the multi-physics simulation toolkit SHARP developed at Argonne National Laboratory, in cooperation with Lawrence Livermore National Laboratory, to simulate the experiment. SHARP uses the spectral element code Nek5000 for fluid dynamics analysis and the finite element code DIABLOmore » for structural analysis. The flow around the coil tubes is modeled in Nek5000 by using a large eddy simulation turbulence model. Transient pressure data on the tube surfaces is sampled and transferred to DIABLO for the structural simulation. The structural response is simulated in DIABLO via an implicit time-marching algorithm and a combination of continuum elements and structural shells. Tube vibration data (acceleration and frequency) are sampled and compared with the experimental data. Currently, only one-way coupling is used, which means that pressure loads from the fluid simulation are transferred to the structural simulation but the resulting structural displacements are not fed back to the fluid simulation.« less

Contribution of proline to the pre-structuring tendency of transient helical secondary structure elements in intrinsically disordered proteins.

PubMed

Lee, Chewook; Kalmar, Lajos; Xue, Bin; Tompa, Peter; Daughdrill, Gary W; Uversky, Vladimir N; Han, Kyou-Hoon

2014-03-01

IDPs function without relying on three-dimensional structures. No clear rationale for such a behavior is available yet. PreSMos are transient secondary structures observed in the target-free IDPs and serve as the target-binding "active" motifs in IDPs. Prolines are frequently found in the flanking regions of PreSMos. Contribution of prolines to the conformational stability of the helical PreSMos in IDPs is investigated. MD simulations are performed for several IDP segments containing a helical PreSMo and the flanking prolines. To measure the influence of flanking-prolines on the structural content of a helical PreSMo calculations were done for wild type as well as for mutant segments with Pro→Asp, His, Lys, or Ala. The change in the helicity due to removal of a proline was measured both for the PreSMo region and for the flanking regions. The α-helical content in ~70% of the helical PreSMos at the early stage of simulation decreases due to replacement of an N-terminal flanking proline by other residues whereas the helix content in nearly all PreSMos increases when the same replacements occur at the C-terminal flanking region. The helix destabilizing/terminating role of the C-terminal flanking prolines is more pronounced than the helix promoting effect of the N-terminal flanking prolines. This work represents a novel example demonstrating that a proline is encoded in an IDP with a defined purpose. The helical PreSMos presage their target-bound conformations. As they most likely mediate IDP-target binding via conformational selection their helical content can be an important feature for IDP function. Copyright © 2013 Elsevier B.V. All rights reserved.

Control of excitons in multi-layer van der Waals heterostructures

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

Calman, E. V., E-mail: ecalman@gmail.com; Dorow, C. J.; Fogler, M. M.

2016-03-07

We report an experimental study of excitons in a double quantum well van der Waals heterostructure made of atomically thin layers of MoS{sub 2} and hexagonal boron nitride. The emission of neutral and charged excitons is controlled by gate voltage, temperature, and both the helicity and the power of optical excitation.

A small hemispherical helical antenna array for two-dimensional GPS beam-forming

NASA Astrophysics Data System (ADS)

Hui, H. T.; Aditya, S.; Mohamed, F. Bin S.; Hafiedz-Ul, A. Bin T.

2005-02-01

A small hemispherical helical antenna array with multibeam output for GPS beam-forming is designed and characterized. A Butler matrix beam-forming network is designed to provide four spatial beams in a two-dimensional directional space. The original design of the hemispherical helical antenna elements is modified in order to match it to the system impedance. Our study shows that even after an ˜30° scan from the normal direction, the maximum change in beam width is only 6°, the maximum change in axial ratio is 1.4 dB, and the maximum change in power gain is 1.1 dB. These characteristics indicate that the array can be potentially used for GPS beam-forming.

Photoproduction of η mesons from the neutron: Cross sections and double polarization observable E

NASA Astrophysics Data System (ADS)

Witthauer, L.; Dieterle, M.; Afzal, F.; Anisovich, A. V.; Bantes, B.; Bayadilov, D.; Beck, R.; Bichow, M.; Brinkmann, K.-T.; Böse, S.; Challand, Th.; Crede, V.; Dutz, H.; Eberhardt, H.; Elsner, D.; Ewald, R.; Fornet-Ponse, K.; Friedrich, St.; Frommberger, F.; Funke, Ch.; Goertz, St.; Gottschall, M.; Gridnev, A.; Grüner, M.; Gutz, E.; Hammann, D.; Hammann, Ch.; Hannappel, J.; Hartmann, J.; Hillert, W.; Hoffmeister, Ph.; Honisch, Ch.; Jude, T.; Kaiser, D.; Kalinowsky, H.; Kalischewski, F.; Kammer, S.; Käser, A.; Keshelashvili, I.; Klassen, P.; Kleber, V.; Klein, F.; Koop, K.; Krusche, B.; Lang, M.; Lopatin, I.; Mahlberg, Ph.; Makonyi, K.; Metag, V.; Meyer, W.; Müller, J.; Müllers, J.; Nanova, M.; Nikonov, V.; Piontek, D.; Reicherz, G.; Rostomyan, T.; Sarantsev, A.; Schmidt, Ch.; Schmieden, H.; Seifen, T.; Sokhoyan, V.; Spieker, K.; Thiel, A.; Thoma, U.; Urban, M.; van Pee, H.; Walford, N. K.; Walther, D.; Wendel, Ch.; Werthmüller, D.; Wilson, A.; Winnebeck, A.

2017-03-01

Results from measurements of the photoproduction of η mesons from quasifree protons and neutrons are summarized. The experiments were performed with the CBELSA/TAPS detector at the electron accelerator ELSA in Bonn using the η→ 3π0→ 6γ decay. A liquid deuterium target was used for the measurement of total cross sections and angular distributions. The results confirm earlier measurements from Bonn and the MAMI facility in Mainz about the existence of a narrow structure in the excitation function of γ n→ nη. The current angular distributions show a forward-backward asymmetry, which was previously not seen, but was predicted by model calculations including an additional narrow P_{11} state. Furthermore, data obtained with a longitudinally polarized, deuterated butanol target and a circularly polarized photon beam were analyzed to determine the double polarization observable E. Both data sets together were also used to extract the helicity-dependent cross sections σ_{1/2} and σ_{3/2}. The narrow structure in the excitation function of γ n→ nη appears associated with the helicity-1/2 component of the reaction.

Radiation hard vacuum switch

DOEpatents

Boettcher, Gordon E.

1990-01-01

A vacuum switch with an isolated trigger probe which is not directly connected to the switching electrodes. The vacuum switch within the plasmatron is triggered by plasma expansion initiated by the trigger probe which travels through an opening to reach the vacuum switch elements. The plasma arc created is directed by the opening to the space between the anode and cathode of the vacuum switch to cause conduction.

A radiation hard vacuum switch

DOEpatents

Boettcher, G.E.

1988-07-19

A vacuum switch with an isolated trigger probe which is not directly connected to the switching electrodes. The vacuum switch within the plasmatron is triggered by plasma expansion initiated by the trigger probe which travels through an opening to reach the vacuum switch elements. The plasma arc created is directed by the opening to the space between the anode and cathode of the vacuum switch to cause conduction. 3 figs.

Radiation hard vacuum switch

DOEpatents

Boettcher, Gordon E.

1990-03-06

A vacuum switch with an isolated trigger probe which is not directly connected to the switching electrodes. The vacuum switch within the plasmatron is triggered by plasma expansion initiated by the trigger probe which travels through an opening to reach the vacuum switch elements. The plasma arc created is directed by the opening to the space between the anode and cathode of the vacuum switch to cause conduction.

Three-dimensional prominence-hosting magnetic configurations: Creating a helical magnetic flux rope

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

Xia, C.; Keppens, R.; Guo, Y.

2014-01-10

The magnetic configuration hosting prominences and their surrounding coronal structure is a key research topic in solar physics. Recent theoretical and observational studies strongly suggest that a helical magnetic flux rope is an essential ingredient to fulfill most of the theoretical and observational requirements for hosting prominences. To understand flux rope formation details and obtain magnetic configurations suitable for future prominence formation studies, we here report on three-dimensional isothermal magnetohydrodynamic simulations including finite gas pressure and gravity. Starting from a magnetohydrostatic corona with a linear force-free bipolar magnetic field, we follow its evolution when introducing vortex flows around the mainmore » polarities and converging flows toward the polarity inversion line near the bottom of the corona. The converging flows bring the feet of different loops together at the polarity inversion line, where magnetic reconnection and flux cancellation happen. Inflow and outflow signatures of the magnetic reconnection process are identified, and thereby the newly formed helical loops wind around preexisting ones so that a complete flux rope grows and ascends. When a macroscopic flux rope is formed, we switch off the driving flows and find that the system relaxes to a stable state containing a helical magnetic flux rope embedded in an overlying arcade structure. A major part of the formed flux rope is threaded by dipped field lines that can stably support prominence matter, while the total mass of the flux rope is in the order of 4-5× 10{sup 14} g.« less

Systems and methods for reducing transient voltage spikes in matrix converters

DOEpatents

Kajouke, Lateef A.; Perisic, Milun; Ransom, Ray M.

2013-06-11

Systems and methods are provided for delivering energy using an energy conversion module that includes one or more switching elements. An exemplary electrical system comprises a DC interface, an AC interface, an isolation module, a first conversion module between the DC interface and the isolation module, and a second conversion module between the AC interface and the isolation module. A control module is configured to operate the first conversion module to provide an injection current to the second conversion module to reduce a magnitude of a current through a switching element of the second conversion module before opening the switching element.

Double-injection, deep-impurity switch development

NASA Technical Reports Server (NTRS)

Selim, F. A.; Whitson, D. W.

1983-01-01

The overall objective of this program is the development of device design and process techniques for the fabrication of a double-injection, deep-impurity (DI)(2) silicon switch that operates in the 1-10 kV range with conduction current of 10 and 1A, respectively. Other major specifications include a holding voltage of 0 to 5 volts at 1 A anode current, 10 microsecond switching time, and power dissipation of 50 W at 75 C. This report describes work that shows how the results obtained at the University of Cincinnati under NASA Grant NSG-3022 have been applied to larger area and higher voltage devices. The investigations include theoretical, analytical, and experimental studies of device design and processing. Methods to introduce deep levels, such as Au diffusion and electron irradiation, have been carried out to "pin down' the Fermi level and control device-switching characteristics. Different anode, cathode, and gate configurations are presented. Techniques to control the surface electric field of planar structures used for (DI)(2) switches are examined. Various sections of this report describe the device design, wafer-processing techniques, and various measurements which include ac and dc characteristics, 4-point probe, and spreading resistance.

Compact, low-loss and low-power 8×8 broadband silicon optical switch.

PubMed

Chen, Long; Chen, Young-kai

2012-08-13

We demonstrated a 8×8 broadband optical switch on silicon for transverse-electrical polarization using a switch-and-selector architecture. The switch has a footprint of only 8 mm × 8 mm, minimum on-chip loss of about 4 dB, and a port-to-port insertion loss variation of only 0.8 dB near some spectral regions. The port-to-port isolation is above 30 dB over the entire 80-nm-wide spectral range or above 45 dB near the central 30 nm. We also demonstrated a switching power of less than 1.5 mW per element and a speed of 2 kHz, and estimated the upper bound of total power consumption to be less than 70 mW even without optimization of the default state of the individual switch elements.

Study on spin filtering and switching action in a double-triangular network chain

NASA Astrophysics Data System (ADS)

Zhang, Yongmei

2018-04-01

Spin transport properties of a double-triangular quantum network with local magnetic moment on backbones and magnetic flux penetrating the network plane are studied. Numerical simulation results show that such a quantum network will be a good candidate for spin filter and spin switch. Local dispersion and density of states are considered in the framework of tight-binding approximation. Transmission coefficients are calculated by the method of transfer matrix. Spin transmission is regulated by substrate magnetic moment and magnetic flux piercing those triangles. Experimental realization of such theoretical research will be conducive to designing of new spintronic devices.

Frequency-doubled passively Q-switched microchip laser producing 225  ps pulses at 671  nm.

PubMed

Nikkinen, Jari; Korpijärvi, Ville-Markus; Leino, Iiro; Härkönen, Antti; Guina, Mircea

2016-11-15

We report a 671 nm laser source emitting 225 ps pulses with an average power of 55 mW and a repetition rate of 444 kHz. The system consists of a 1342 nm SESAM Q-switched Nd:YVO₄ microchip master oscillator and a dual-stage Nd:YVO₄ power amplifier. The 1342 nm signal was frequency-doubled to 671 nm using a periodically poled lithium niobate crystal. This laser source provides a practical alternative for applications requiring high energy picosecond pulses, such as time-gated Raman spectroscopy.

S46 Peptidases are the First Exopeptidases to be Members of Clan PA

PubMed Central

Sakamoto, Yasumitsu; Suzuki, Yoshiyuki; Iizuka, Ippei; Tateoka, Chika; Roppongi, Saori; Fujimoto, Mayu; Inaka, Koji; Tanaka, Hiroaki; Masaki, Mika; Ohta, Kazunori; Okada, Hirofumi; Nonaka, Takamasa; Morikawa, Yasushi; Nakamura, Kazuo T.; Ogasawara, Wataru; Tanaka, Nobutada

2014-01-01

The dipeptidyl aminopeptidase BII (DAP BII) belongs to a serine peptidase family, S46. The amino acid sequence of the catalytic unit of DAP BII exhibits significant similarity to those of clan PA endopeptidases, such as chymotrypsin. However, the molecular mechanism of the exopeptidase activity of family S46 peptidase is unknown. Here, we report crystal structures of DAP BII. DAP BII contains a peptidase domain including a typical double β-barrel fold and previously unreported α-helical domain. The structures of peptide complexes revealed that the α-helical domain covers the active-site cleft and the side chain of Asn330 in the domain forms hydrogen bonds with the N-terminus of the bound peptide. These observations indicate that the α-helical domain regulates the exopeptidase activity of DAP BII. Because S46 peptidases are not found in mammals, we expect that our study will be useful for the design of specific inhibitors of S46 peptidases from pathogens. PMID:24827749

Dissociable effects of game elements on motivation and cognition in a task-switching training in middle childhood

PubMed Central

Dörrenbächer, Sandra; Müller, Philipp M.; Tröger, Johannes; Kray, Jutta

2014-01-01

Although motivational reinforcers are often used to enhance the attractiveness of trainings of cognitive control in children, little is known about how such motivational manipulations of the setting contribute to separate gains in motivation and cognitive-control performance. Here we provide a framework for systematically investigating the impact of a motivational video-game setting on the training motivation, the task performance, and the transfer success in a task-switching training in middle-aged children (8–11 years of age). We manipulated both the type of training (low-demanding/single-task training vs. high-demanding/task-switching training) as well as the motivational setting (low-motivational/without video-game elements vs. high-motivational/with video-game elements) separately from another. The results indicated that the addition of game elements to a training setting enhanced the intrinsic interest in task practice, independently of the cognitive demands placed by the training type. In the task-switching group, the high-motivational training setting led to an additional enhancement of task and switching performance during the training phase right from the outset. These motivation-induced benefits projected onto the switching performance in a switching situation different from the trained one (near-transfer measurement). However, in structurally dissimilar cognitive tasks (far-transfer measurement), the motivational gains only transferred to the response dynamics (speed of processing). Hence, the motivational setting clearly had a positive impact on the training motivation and on the paradigm-specific task-switching abilities; it did not, however, consistently generalize on broad cognitive processes. These findings shed new light on the conflation of motivation and cognition in childhood and may help to refine guidelines for designing adequate training interventions. PMID:25431564

On-Board Switching and Routing Advanced Technology Study

NASA Technical Reports Server (NTRS)

Yegenoglu, F.; Inukai, T.; Kaplan, T.; Redman, W.; Mitchell, C.

1998-01-01

Future satellite communications is expected to be fully integrated into National and Global Information Infrastructures (NII/GII). These infrastructures will carry multi gigabit-per-second data rates, with integral switching and routing of constituent data elements. The satellite portion of these infrastructures must, therefore, be more than pipes through the sky. The satellite portion will also be required to perform very high speed routing and switching of these data elements to enable efficient broad area coverage to many home and corporate users. The technology to achieve the on-board switching and routing must be selected and developed specifically for satellite application within the next few years. This report presents evaluation of potential technologies for on-board switching and routing applications.

Denoising of genetic switches based on Parrondo's paradox

NASA Astrophysics Data System (ADS)

Fotoohinasab, Atiyeh; Fatemizadeh, Emad; Pezeshk, Hamid; Sadeghi, Mehdi

2018-03-01

Random decision making in genetic switches can be modeled as tossing a biased coin. In other word, each genetic switch can be considered as a game in which the reactive elements compete with each other to increase their molecular concentrations. The existence of a very small number of reactive element molecules has caused the neglect of effects of noise to be inevitable. Noise can lead to undesirable cell fate in cellular differentiation processes. In this paper, we study the robustness to noise in genetic switches by considering another switch to have a new gene regulatory network (GRN) in which both switches have been affected by the same noise and for this purpose, we will use Parrondo's paradox. We introduce two networks of games based on possible regulatory relations between genes. Our results show that the robustness to noise can increase by combining these noisy switches. We also describe how one of the switches in network II can model lysis/lysogeny decision making of bacteriophage lambda in Escherichia coli and we change its fate by another switch.

An updated version of NPIDB includes new classifications of DNA–protein complexes and their families

PubMed Central

Zanegina, Olga; Kirsanov, Dmitriy; Baulin, Eugene; Karyagina, Anna; Alexeevski, Andrei; Spirin, Sergey

2016-01-01

The recent upgrade of nucleic acid–protein interaction database (NPIDB, http://npidb.belozersky.msu.ru/) includes a newly elaborated classification of complexes of protein domains with double-stranded DNA and a classification of families of related complexes. Our classifications are based on contacting structural elements of both DNA: the major groove, the minor groove and the backbone; and protein: helices, beta-strands and unstructured segments. We took into account both hydrogen bonds and hydrophobic interaction. The analyzed material contains 1942 structures of protein domains from 748 PDB entries. We have identified 97 interaction modes of individual protein domain–DNA complexes and 17 DNA–protein interaction classes of protein domain families. We analyzed the sources of diversity of DNA–protein interaction modes in different complexes of one protein domain family. The observed interaction mode is sometimes influenced by artifacts of crystallization or diversity in secondary structure assignment. The interaction classes of domain families are more stable and thus possess more biological sense than a classification of single complexes. Integration of the classification into NPIDB allows the user to browse the database according to the interacting structural elements of DNA and protein molecules. For each family, we present average DNA shape parameters in contact zones with domains of the family. PMID:26656949

Helix coupling

DOEpatents

Ginell, W.S.

1982-03-17

A coupling for connecting helix members in series, which consists of a pair of U-shaped elements, one of which is attached to each helix end with the U sections of the elements interlocked. The coupling is particularly beneficial for interconnecting helical Nitinol elements utilized in thermal actuators or engines. Each coupling half is attached to the associated helix at two points, thereby providing axial load while being easily removed from the helix, and reusable.

Helix coupling

DOEpatents

Ginell, William S.

1989-04-25

A coupling for connecting helix members in series, which consists of a pair of U-shaped elements, one of which is attached to each helix end with the "U" sections of the elements interlocked. The coupling is particularly beneficial for interconnecting helical Nitinol elements utilized in thermal actuators or engines. Each coupling half is attached to the associated helix at two points, thereby providing axial load while being easily removed from the helix, and reusable.

Ultralow power switching in a silicon-rich SiNy/SiNx double-layer resistive memory device.

PubMed

Kim, Sungjun; Chang, Yao-Feng; Kim, Min-Hwi; Bang, Suhyun; Kim, Tae-Hyeon; Chen, Ying-Chen; Lee, Jong-Ho; Park, Byung-Gook

2017-07-26

Here we demonstrate low-power resistive switching in a Ni/SiN y /SiN x /p ++ -Si device by proposing a double-layered structure (SiN y /SiN x ), where the two SiN layers have different trap densities. The LRS was measured to be as low as 1 nA at a voltage of 1 V, because the SiN x layer maintains insulating properties for the LRS. The single-layered device suffers from uncontrollability of the conducting path, accompanied by the inherent randomness of switching parameters, weak immunity to breakdown during the reset process, and a high operating current. On the other hand, for a double-layered device, the effective conducting path in each layer, which can determine the operating current, can be well controlled by the I CC during the initial forming and set processes. A one-step forming and progressive reset process is observed for a low-power mode, which differs from the high-power switching mode that shows a two-step forming and reset process. Moreover, nonlinear behavior in the LRS, whose origin can be attributed to the P-F conduction and F-N tunneling driven by abundant traps in the silicon-rich SiN x layer, would be beneficial for next-generation nonvolatile memory applications by using a conventional passive SiN x layer as an active dielectric.

Response characteristic of high-speed on/off valve with double voltage driving circuit

NASA Astrophysics Data System (ADS)

Li, P. X.; Su, M.; Zhang, D. B.

2017-07-01

High-speed on/off valve, an important part of turbocharging system, its quick response has a direct impact on the turbocharger pressure cycle. The methods of improving the response characteristic of high speed on/off valve include increasing the magnetic force of armature and the voltage, decreasing the mass and current of coil. The less coil number of turns, the solenoid force is smaller. The special armature structure and the magnetic material will raise cost. In this paper a new scheme of double voltage driving circuit is investigated, in which the original driving circuit of high-speed on/off valve is replaced by double voltage driving circuit. The detailed theoretical analysis and simulations were carried out on the double voltage driving circuit, it showed that the switching time and delay time of the valve respectively are 3.3ms, 5.3ms, 1.9ms and 1.8ms. When it is driven by the double voltage driving circuit, the switching time and delay time of this valve are reduced, optimizing its response characteristic. By the comparison related factors (such as duty cycle or working frequency) about influences on response characteristic, the superior of double voltage driving circuit has been further confirmed.

Hyperswitch Network For Hypercube Computer

NASA Technical Reports Server (NTRS)

Chow, Edward; Madan, Herbert; Peterson, John

1989-01-01

Data-driven dynamic switching enables high speed data transfer. Proposed hyperswitch network based on mixed static and dynamic topologies. Routing header modified in response to congestion or faults encountered as path established. Static topology meets requirement if nodes have switching elements that perform necessary routing header revisions dynamically. Hypercube topology now being implemented with switching element in each computer node aimed at designing very-richly-interconnected multicomputer system. Interconnection network connects great number of small computer nodes, using fixed hypercube topology, characterized by point-to-point links between nodes.

Polarized Kink Waves in Magnetic Elements: Evidence for Chromospheric Helical Waves

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

Stangalini, M.; Giannattasio, F.; Erdélyi, R.

In recent years, new high spatial resolution observations of the Sun's atmosphere have revealed the presence of a plethora of small-scale magnetic elements down to the resolution limit of the current cohort of solar telescopes (∼100–120 km on the solar photosphere). These small magnetic field concentrations, due to the granular buffeting, can support and guide several magnetohydrodynamic wave modes that would eventually contribute to the energy budget of the upper layers of the atmosphere. In this work, exploiting the high spatial and temporal resolution chromospheric data acquired with the Swedish 1 m Solar Telescope, and applying the empirical mode decompositionmore » technique to the tracking of the solar magnetic features, we analyze the perturbations of the horizontal velocity vector of a set of chromospheric magnetic elements. We find observational evidence that suggests a phase relation between the two components of the velocity vector itself, resulting in its helical motion.« less

Seven 3d-4f coordination polymers of macrocyclic oxamide with polycarboxylates: Syntheses, crystal structures and magnetic properties

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

Xin, Na; Key Laboratory of Inorganic-Organic Hybrid Functional Material Chemistry, Ministry of Education; Tianjin Key Laboratory of Structure and Performance for Functional Molecules

2016-11-15

Seven new 3d–4f heterometallic coordination polymers, [Ln(CuL){sub 2}(Hbtca)(btca)(H{sub 2}O)]·2H{sub 2}O (Ln = Tb{sup III}1, Pr{sup III}2, Sm{sup III}3, Eu{sup III}4, Yb{sup III}5), [Nd(NiL)(nip)(Rnip)]·0·25H{sub 2}O·0.25CH{sub 3}OH (R= 0.6CH{sub 3}, 0.4H) 6 and [Nd{sub 2}(NiL)(nip){sub 3}(H{sub 2}O)]·2H{sub 2}O 7(CuL or NiL, H{sub 2}L = 2, 3-dioxo-5, 6, 14, 15-dibenzo-1, 4, 8, 12-tetraazacyclo-pentadeca-7, 13-dien; H{sub 2}btca = benzotriazole-5-carboxylic acid; H{sub 2}nip = 5-nitroisophthalic acid) have been synthesized by a solvothermal method and characterized by single-crystal X-ray diffraction. Complexes 1–5 exhibit a double-strand meso-helical chain structures formed by [Ln{sup III}Cu{sup II}{sub 2}] units via the oxamide and benzotriazole-5-carboxylate bridges, while complex 6 exhibits amore » four-strand meso-helical chain formed by NdNi unit via the oxamide and 5-nitroisophthalate bridges. Complex 7 consists of a 2D layer framework formed by four-strand meso-helical chain via the nip{sup 2−} bridges. Moreover, the magnetic properties of them were investigated, and the best-fit analysis of χ{sub M}T versus T show that the anisotropic contribution of Ln(III) ions (arising from the spin-orbit coupling or the crystal field perturbation) dominates (weak exchange limit) in these complexes(for 3, λ = 214.6 cm{sup −1}, zj’ = −0.33 cm{sup −1}, g{sub av} = 1.94; for 5, Δ = 6.98 cm{sup −1}, zj’ = 1.53 cm{sup −1}, g{sub av} = 1.85). - Graphical-abstract: Seven novel oxamido-bridged 3d-4f heterometallic coordination polymers with benzotriazole-5-carboxylate or 5-nitroisophthalate co-ligands under solvothermal reaction conditions. Polymers 1–7 hold 1D or 2D framework structure, viz., double-strand meso-helical chain of 1–5, four-strand meso-helical chain of 6, and 2D net of 7 consisting of four-strand meso-helical chain. Moreover, the temperature dependences of magnetic susceptibilities of compounds 1–7 were also studied.« less

A Multicontrolled Enamine Configurational Switch Undergoing Dynamic Constitutional Exchange.

PubMed

Ren, Yansong; Svensson, Per H; Ramström, Olof

2018-05-22

A multiresponsive enamine-based molecular switch is presented, in which forward/backward configurational rotation around the C=C bond could be precisely controlled by the addition of an acid/base or metal ions. Fluorescence turn-on/off effects and large Stokes shifts were observed while regulating the switching process with Cu II . The enamine functionality furthermore enabled double dynamic regimes, in which configurational switching could operate in conjunction with constitutional enamine exchange of the rotor part. This behavior was used to construct a prototypical dynamic covalent switch system through enamine exchange with primary amines. The dynamic exchange process could be readily turned on/off by regulating the switch status with pH. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Study on the criterion to determine the bottom deployment modes of a coilable mast

NASA Astrophysics Data System (ADS)

Ma, Haibo; Huang, Hai; Han, Jianbin; Zhang, Wei; Wang, Xinsheng

2017-12-01

A practical design criterion that allows the coilable mast bottom to deploy in local coil mode was proposed. The criterion was defined with initial bottom helical angle and obtained by bottom deformation analyses. Discretizing the longerons into short rods, analyses were conducted based on the cylinder assumption and Kirchhoff's kinetic analogy theory. Then, iterative calculations aiming at the bottom four rods were carried out. A critical bottom helical angle was obtained while the angle changing rate equaled to zero. The critical value was defined as a criterion for judgement of bottom deployment mode. Subsequently, micro-gravity deployment tests were carried out and bottom deployment simulations based on finite element method were developed. Through comparisons of bottom helical angles in critical state, the proposed criterion was evaluated and modified, that is, an initial bottom helical angle less than critical value with a design margin of -13.7% could ensure the mast bottom deploying in local coil mode, and further determine a successful local coil deployment of entire coilable mast.

Electronic switching circuit uses complementary non-linear components

NASA Technical Reports Server (NTRS)

Zucker, O. S.

1972-01-01

Inherent switching properties of saturable inductors and storage diodes are combined to perform large variety of electronic functions, such as pulse shaping, gating, and multiplexing. Passive elements replace active switching devices in generation of complex waveforms.

Control of single-electron charging of metallic nanoparticles onto amorphous silicon surface.

PubMed

Weis, Martin; Gmucová, Katarína; Nádazdy, Vojtech; Capek, Ignác; Satka, Alexander; Kopáni, Martin; Cirák, Július; Majková, Eva

2008-11-01

Sequential single-electron charging of iron oxide nanoparticles encapsulated in oleic acid/oleyl amine envelope and deposited by the Langmuir-Blodgett technique onto Pt electrode covered with undoped hydrogenated amorphous silicon film is reported. Single-electron charging (so-called quantized double-layer charging) of nanoparticles is detected by cyclic voltammetry as current peaks and the charging effect can be switched on/off by the electric field in the surface region induced by the excess of negative/positive charged defect states in the amorphous silicon layer. The particular charge states in amorphous silicon are created by the simultaneous application of a suitable bias voltage and illumination before the measurement. The influence of charged states on the electric field in the surface region is evaluated by the finite element method. The single-electron charging is analyzed by the standard quantized double layer model as well as two weak-link junctions model. Both approaches are in accordance with experiment and confirm single-electron charging by tunnelling process at room temperature. This experiment illustrates the possibility of the creation of a voltage-controlled capacitor for nanotechnology.

Calibrating pressure switch

NASA Technical Reports Server (NTRS)

Smith, N. J. (Inventor)

1968-01-01

A pressure switch assembly comprising a body portion and a switch mechanism having a contact element operable between opposite limit positions is described. A diaphragm chamber is provided in the body portion which mounts therein a system diaphragm and a calibration diaphragm which are of generally the same configuration and having outer faces conforming to the inner and outer walls of the diaphragm chamber. The space between the inner faces of the diaphragms defines a first chamber section and the space between the outer face of one of the diaphragms and the outer wall of the diaphragm chamber defines a second chamber section. The body portion includes a system pressure port communicating with one of the chamber sections and a calibration pressure port communicating with the other chamber section. An actuator connected to one of the diaphragms and the contact element of the switch operates upon pressure change in the diaphragm sections to move said contact element between limit positions.

Ligand-mediated and tertiary interactions cooperatively stabilize the P1 region in the guanine-sensing riboswitch

PubMed Central

Hanke, Christian A.

2017-01-01

Riboswitches are genetic regulatory elements that control gene expression depending on ligand binding. The guanine-sensing riboswitch (Gsw) binds ligands at a three-way junction formed by paired regions P1, P2, and P3. Loops L2 and L3 cap the P2 and P3 helices and form tertiary interactions. Part of P1 belongs to the switching sequence dictating the fate of the mRNA. Previous studies revealed an intricate relationship between ligand binding and presence of the tertiary interactions, and between ligand binding and influence on the P1 region. However, no information is available on the interplay among these three main regions in Gsw. Here we show that stabilization of the L2-L3 region by tertiary interactions, and the ligand binding site by ligand binding, cooperatively influences the structural stability of terminal base pairs in the P1 region in the presence of Mg2+ ions. The results are based on molecular dynamics simulations with an aggregate simulation time of ~10 μs across multiple systems of the unbound state of the Gsw aptamer and a G37A/C61U mutant, and rigidity analyses. The results could explain why the three-way junction is a central structural element also in other riboswitches and how the cooperative effect could become contextual with respect to intracellular Mg2+ concentration. The results suggest that the transmission of allosteric information to P1 can be entropy-dominated. PMID:28640851

The chemical end-ligation of homopyrimidine oligodeoxyribonucleotides within a DNA triple helix.

PubMed

Li, T; Weinstein, D S; Nicolaou, K

1997-03-01

Triple-helical nucleic acids, first reported in the late 1950s, are receiving attention for their possible involvement in controlling gene expression. Certain sequences of DNA are believed to form local triple-helical structures (H-form DNA), although this has not been directly observed in vivo. Studies carried out in our laboratories have suggested that self-replicating oligonucleotides could have been involved in chemical evolution via triple-helical intermediates. In addition to self-replication mechanisms, elucidating processes for the nonenzymatic elongation of biologically relevant polymers remains an important challenge in understanding the origin of life. To this end, we have studied a novel ligation of oligodeoxyribonucleotides that lie within a triple helix. The chemical end-ligation of homopyrimidine oligodeoxyribonucleotides on a triple helix is reported. This selective process, induced by cyanoimidazole, is facilitated by a template effect of the DNA aggregate and occurs between the 3' end (hydroxyl) of the third minor-groove-bound strand and the 5' end (phosphate) of the antiparallel oligopyrimidine strand. Double-helical homopurine/homopyrimidine DNA can serve as a template for the elongation of oligonucleotides in a manner that has not been described previously. The end-ligation of homopyrimidine oligomers, a nonenzymatic process, proceeds via a requisite triple-helical intermediate and constitutes an efficient and selective method for the template-directed elongation of nucleic acids. Such a process could conceivably have been involved in the elongation of primordial information-bearing biopolymers.

Random single amino acid deletion sampling unveils structural tolerance and the benefits of helical registry shift on GFP folding and structure.

PubMed

Arpino, James A J; Reddington, Samuel C; Halliwell, Lisa M; Rizkallah, Pierre J; Jones, D Dafydd

2014-06-10

Altering a protein's backbone through amino acid deletion is a common evolutionary mutational mechanism, but is generally ignored during protein engineering primarily because its effect on the folding-structure-function relationship is difficult to predict. Using directed evolution, enhanced green fluorescent protein (EGFP) was observed to tolerate residue deletion across the breadth of the protein, particularly within short and long loops, helical elements, and at the termini of strands. A variant with G4 removed from a helix (EGFP(G4Δ)) conferred significantly higher cellular fluorescence. Folding analysis revealed that EGFP(G4Δ) retained more structure upon unfolding and refolded with almost 100% efficiency but at the expense of thermodynamic stability. The EGFP(G4Δ) structure revealed that G4 deletion caused a beneficial helical registry shift resulting in a new polar interaction network, which potentially stabilizes a cis proline peptide bond and links secondary structure elements. Thus, deletion mutations and registry shifts can enhance proteins through structural rearrangements not possible by substitution mutations alone. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

DNA Structure and Supercoiling: Ribbons and a Yo-Yo Model

ERIC Educational Resources Information Center

Van Horn, J. David

2011-01-01

The double-helical structure of DNA is a pop cultural icon. Images of the DNA molecule appear in newspapers, popular journals, and advertisements. In addition to scientific instrument sales, the aura surrounding the central molecule of life has been used to sell everything from perfume to beverages and is the inspiration of items ranging from…

Double Charge Exchange Reactions and Double Beta Decay

NASA Astrophysics Data System (ADS)

Auerbach, N.

2018-05-01

The subject of this presentation is at the forefront of nuclear physics, namely double beta decay. In particular one is most interested in the neutrinoless process of double beta decay, when the decay proceeds without the emission of two neutrinos. The observation of such decay would mean that the lepton conservation symmetry is violated and that the neutrinos are of Majorana type, meaning that they are their own anti-particles. The life time of this process has two unknowns, the mass of the neutrino and the nuclear matrix element. Determining the nuclear matrix element and knowing the cross-section well will set limits on the neutrino mass. There is a concentrated effort among the nuclear physics community to calculate this matrix element. Usually these matrix elements are a very small part of the total strength of the transition operators involved in the process. There is no simple way to “calibrate” the nuclear double beta decay matrix element. The double beta decay is a double charge exchange process, therefore it is proposed that double charge exchange reactions using ion projectiles on nuclei that are candidates for double beta decay, will provide additional necessary information about the nuclear matrix elements.

Passively Q-switched, intracavity frequency-doubled YVO{sub 4}/Nd : YVO{sub 4}/KTP green laser with a GaAs saturable absorber

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

Shang Gao

2015-11-30

A diode-pumped, passively Q-switched, intracavity frequency-doubled YVO{sub 4}/Nd : YVO{sub 4}/KTP green laser is realised using a GaAs saturable absorber. Two pieces of GaAs wafers are employed in the experiment. In using a 400-μm-thick GaAs wafer and an incident pump power of 10.5 W, the maximum output power of the passively Q-switched green laser is 362 mW at a pulse repetition rate of 84 kHz and a pulse duration of 2.5 ns. When use is made of a 700-mm-thick GaAs wafer, the minimum pulse duration is 1.5 ns at a repetition rate of 67 kHz, pulse energy of 4.18 μJmore » and peak power of 2.8 kW. (control of laser radiation parameters)« less

Monolithically integrated all-optical gate switch using intersubband transition in InGaAs/AlAsSb coupled double quantum wells.

PubMed

Akimoto, Ryoichi; Gozu, Shin-ichiro; Mozume, Teruo; Ishikawa, Hiroshi

2011-07-04

We have developed a compact all-optical gate switch with a footprint less than 1 mm2, in which an optical nonlinear waveguide using cross-phase-modulation associated with intersubband transition in InGaAs/AlGaAs/AlAsSb coupled double quantum wells and a Michelson interferometer (MI) are monolithically integrated on an InP chip. The MI configuration allows a transverse magnetic pump light direct access to an MI arm for phase modulation while passive photonic integrated circuits serve a transverse electric signal light. Full switching of the π-rad nonlinear phase shift is achieved with a pump pulse energy of 8.6 pJ at a 10-GHz repetition rate. We also demonstrate all-optical demultiplexing of a 160-Gb/s signal to a 40-Gb/s signal.

Designing pH induced fold switch in proteins

NASA Astrophysics Data System (ADS)

Baruah, Anupaul; Biswas, Parbati

2015-05-01

This work investigates the computational design of a pH induced protein fold switch based on a self-consistent mean-field approach by identifying the ensemble averaged characteristics of sequences that encode a fold switch. The primary challenge to balance the alternative sets of interactions present in both target structures is overcome by simultaneously optimizing two foldability criteria corresponding to two target structures. The change in pH is modeled by altering the residual charge on the amino acids. The energy landscape of the fold switch protein is found to be double funneled. The fold switch sequences stabilize the interactions of the sites with similar relative surface accessibility in both target structures. Fold switch sequences have low sequence complexity and hence lower sequence entropy. The pH induced fold switch is mediated by attractive electrostatic interactions rather than hydrophobic-hydrophobic contacts. This study may provide valuable insights to the design of fold switch proteins.

Finite element based contact analysis of radio frequency MEMs switch membrane surfaces

NASA Astrophysics Data System (ADS)

Liu, Jin-Ya; Chalivendra, Vijaya; Huang, Wenzhen

2017-10-01

Finite element simulations were performed to determine the contact behavior of radio frequency (RF) micro-electro-mechanical (MEM) switch contact surfaces under monotonic and cyclic loading conditions. Atomic force microscopy (AFM) was used to capture the topography of RF-MEM switch membranes and later they were analyzed for multi-scale regular as well as fractal structures. Frictionless, non-adhesive contact 3D finite element analysis was carried out at different length scales to investigate the contact behavior of the regular-fractal surface using an elasto-plastic material model. Dominant micro-scale regular patterns were found to significantly change the contact behavior. Contact areas mainly cluster around the regular pattern. The contribution from the fractal structure is not significant. Under cyclic loading conditions, plastic deformation in the 1st loading/unloading cycle smooth the surface. The subsequent repetitive loading/unloading cycles undergo elastic contact without changing the morphology of the contacting surfaces. The work is expected to shed light on the quality of the switch surface contact as well as the optimum design of RF MEM switch surfaces.

Age differences in working memory updating: the role of interference, focus switching and substituting information.

PubMed

Lendínez, Cristina; Pelegrina, Santiago; Lechuga, M Teresa

2015-05-01

Working memory updating (WMU) tasks require different elements in working memory (WM) to be maintained simultaneously, accessing one of these elements, and substituting its content. This study examined possible developmental changes from childhood to adulthood both in focus switching and substituting information in WM. In addition, possible age-related changes in interference due to representational overlap between the different elements simultaneously held in these tasks were examined. Children (8- and 11-year-olds), adolescents (14-year-olds) and younger adults (mean age=22 years) were administered a numerical updating memory task, in which updating and focus switching were manipulated. As expected, response times decreased and recall performance increased with age. More importantly, the time needed for focus switching was longer in children than in adolescents and younger adults. On the other hand, substitution of information and interference due to representational overlap were not affected by age. These results suggest that age-related changes in focus switching might mediate developmental changes in WMU performance. Copyright © 2015 Elsevier B.V. All rights reserved.

Lack of ubiquitin immunoreactivities at both ends of neuropil threads. Possible bidirectional growth of neuropil threads.

PubMed

Iwatsubo, T; Hasegawa, M; Esaki, Y; Ihara, Y

1992-02-01

Immunocytochemically, neuropil threads (curly fibers) were investigated in the Alzheimer's disease brain using a confocal laser scanning fluorescence microscope by double labeling with tau/ubiquitin antibodies. Ubiquitin immunoreactivities were found to be lacking at one or both ends in more than 40% of tau-positive threads. Immunoelectron microscopy showed that bundles of paired helical filaments, which constitute neuropil threads, were positive for ubiquitin around their midportions, but often negative at their ends. Since it is reasonable to postulate that tau deposition as paired helical filaments precedes ubiquitination, the aforementioned observation suggests that the ends of the threads are newly formed portions, and thus the threads are often growing bidirectionally in small neuronal processes.

Effects of dielectric inhomogeneity on electrostatic twist rigidity of a helical biomolecule in Debye-Hückel regime

NASA Astrophysics Data System (ADS)

Rezaie-Dereshgi, Amir; Mohammad-Rafiee, Farshid

2018-04-01

The electrostatic interactions play a crucial role in biological systems. Here we consider an impermeable dielectric molecule in the solvent with a different dielectric constant. The electrostatic free energy in the problem is studied in the Debye-Hückel regime using the analytical Green function that is calculated in the paper. Using this electrostatic free energy, we study the electrostatic contribution to the twist rigidity of a double stranded helical molecule such as a DNA and an actin filament. The dependence of the electrostatic twist rigidity of the molecule to the dielectric inhomogeneity, structural parameters, and the salt concentration is studied. It is shown that, depending on the parameters, the electrostatic twist rigidity could be positive or negative.

Nucleic acid duplexes incorporating a dissociable covalent base pair

NASA Technical Reports Server (NTRS)

Gao, K.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

1999-01-01

We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure.

Thermodynamic characterization of a triple-helical three-way junction containing a Hoogsteen branch point.

PubMed

Hüsler, P L; Klump, H H

1995-09-10

We have designed a Hoogsteen (HG) triple-helical three-way junction (ternary complex) constructed from three 33-mer oligonucleotides based on the same subset of sequences used for the Watson-Crick (WC) triple-helical three-way junction, characterized previously (P. L. Hüsler and H. H. Klump (1994) Arch. Biochem. Biophys., 313, 29-38). The junction differs primarily in the assembly of the branch point and the ends of the arms. The three oligonucleotides can each fold into a WC hairpin, linked by a four-member cytosine loop, each containing a homo-pyrimidine 10-mer single-strand extension. On lowering the pH (between 6 and 4), the extensions mutually associate to one of the other hairpins via Hoogsteen (HG) hydrogen bonding. Collectively, this process results in the formation of the branch point and the triple-helical arms. The HG triple-helical three-way junction is characterized by gel electrophoresis, circular dichroism, uv melting, and differential scanning calorimetry. The junction undergoes thermal unfolding in two distinct temperature regions. In the temperature range 15 to 50 degrees C loss of HG base pairing results in the dissociation of the three-way junction. Between 55 and 95 degrees C the resulting hairpins undergo further successive unfolding. The overall calorimetric unfolding enthalpy and entropy changes associated with the loss of HG base pairing are approximately equal to the sum of the enthalpy and entropy changes associated with the dissociation of the HG base pairing in the isolated arms (170.6 kcal.mol-1; 540.1 cal.mol-1.K-1). It is apparent from these results that in the proximity of the branch point the structure is not perturb or strain. This result is contrary to the results obtained for the WC triple-helical three-way and for three-way junctions constructed from canonical double-helical DNA. Complete folding of the junction requires either high Na+ (600 mM) ion concentrations or 40-60 mM Mg2+.

alpha-helical structural elements within the voltage-sensing domains of a K(+) channel.

PubMed

Li-Smerin, Y; Hackos, D H; Swartz, K J

2000-01-01

Voltage-gated K(+) channels are tetramers with each subunit containing six (S1-S6) putative membrane spanning segments. The fifth through sixth transmembrane segments (S5-S6) from each of four subunits assemble to form a central pore domain. A growing body of evidence suggests that the first four segments (S1-S4) comprise a domain-like voltage-sensing structure. While the topology of this region is reasonably well defined, the secondary and tertiary structures of these transmembrane segments are not. To explore the secondary structure of the voltage-sensing domains, we used alanine-scanning mutagenesis through the region encompassing the first four transmembrane segments in the drk1 voltage-gated K(+) channel. We examined the mutation-induced perturbation in gating free energy for periodicity characteristic of alpha-helices. Our results are consistent with at least portions of S1, S2, S3, and S4 adopting alpha-helical secondary structure. In addition, both the S1-S2 and S3-S4 linkers exhibited substantial helical character. The distribution of gating perturbations for S1 and S2 suggest that these two helices interact primarily with two environments. In contrast, the distribution of perturbations for S3 and S4 were more complex, suggesting that the latter two helices make more extensive protein contacts, possibly interfacing directly with the shell of the pore domain.

Optical fiber loops and helices: tools for integrated photonic device characterization and microfluidic trapping

NASA Astrophysics Data System (ADS)

Ren, Yundong; Zhang, Rui; Ti, Chaoyang; Liu, Yuxiang

2016-09-01

Tapered optical fibers can deliver guided light into and carry light out of micro/nanoscale systems with low loss and high spatial resolution, which makes them ideal tools in integrated photonics and microfluidics. Special geometries of tapered fibers are desired for probing monolithic devices in plane as well as optical manipulation of micro particles in fluids. However, for many specially shaped tapered fibers, it remains a challenge to fabricate them in a straightforward, controllable, and repeatable way. In this work, we fabricated and characterized two special geometries of tapered optical fibers, namely fiber loops and helices, that could be switched between one and the other. The fiber loops in this work are distinct from previous ones in terms of their superior mechanical stability and high optical quality factors in air, thanks to a post-annealing process. We experimentally measured an intrinsic optical quality factor of 32,500 and a finesse of 137 from a fiber loop. A fiber helix was used to characterize a monolithic cavity optomechanical device. Moreover, a microfluidic "roller coaster" was demonstrated, where microscale particles in water were optically trapped and transported by a fiber helix. Tapered fiber loops and helices can find various applications ranging from on-the-fly characterization of integrated photonic devices to particle manipulation and sorting in microfluidics.

Low-frequency approximation for high-order harmonic generation by a bicircular laser field

NASA Astrophysics Data System (ADS)

Milošević, D. B.

2018-01-01

We present low-frequency approximation (LFA) for high-order harmonic generation (HHG) process. LFA represents the lowest-order term of an expansion of the final-state interaction matrix element in powers of the laser-field frequency ω . In this approximation the plane-wave recombination matrix element which appears in the strong-field approximation is replaced by the exact laser-free recombination matrix element calculated for the laser-field dressed electron momenta. First, we have shown that the HHG spectra obtained using the LFA agree with those obtained solving the time-dependent Schrödinger equation. Next, we have applied this LFA to calculate the HHG rate for inert gases exposed to a bicircular field. The bicircular field, which consists of two coplanar counter-rotating fields having different frequencies (usually ω and 2 ω ), is presently an important subject of scientific research since it enables efficient generation of circularly polarized high-order harmonics (coherent soft x rays). Analyzing the photorecombination matrix element we have found that the HHG rate can efficiently be calculated using the angular momentum basis with the states oriented in the direction of the bicircular field components. Our numerical results show that the HHG rate for atoms having p ground state, for higher high-order harmonic energies, is larger for circularly polarized harmonics having the helicity -1 . For lower energies the harmonics having helicity +1 prevails. The transition between these two harmonic energy regions can appear near the Cooper minimum, which, in the case of Ar atoms, makes the selection of high-order harmonics having the same helicity much easier. This is important for applications (for example, for generation of attosecond pulse trains of circularly polarized harmonics).

Three-dimensional ceramic molding process based on microstereolithography for the production of piezoelectric energy harvesters

NASA Astrophysics Data System (ADS)

Maruo, Shoji; Sugiyama, Kenji; Daicho, Yuya; Monri, Kensaku

2014-03-01

A three-dimensional (3-D) molding process using a master polymer mold produced by microstereolithography has been developed for the production of piezoelectric ceramic elements. In this method, ceramic slurry is injected into a 3-D polymer mold via a centrifugal casting process. The polymer master mold is thermally decomposed so that complex 3-D piezoelectric ceramic elements can be produced. As an example of 3-D piezoelectric ceramic elements, we produced a spiral piezoelectric element that can convert multidirectional loads into a voltage. It was confirmed that a prototype of the spiral piezoelectric element could generate a voltage by applying a load in both parallel and lateral directions in relation to the helical axis. The power output of 123 pW was obtained by applying the maximum load of 2.8N at 2 Hz along the helical axis. In addition, to improve the performance of power generation, we utilized a two-step sintering process to obtain dense piezoelectric elements. As a result, we obtained a sintering body with relative density of 92.8%. Piezoelectric constant d31 of the sintered body attained to -40.0 pC/N. Furthermore we analyzed the open-circuit voltage of the spiral piezoelectric element using COMSOL multiphysics. As a result, it was found that use of patterned electrodes according to the surface potential distribution of the spiral piezoelectric element had a potential to provide high output voltage that was 20 times larger than that of uniform electrodes.

Electromyographic Analysis of the Peroneous Longus during Bicycle Ergometry across Work Load and Pedal Type.

DTIC Science & Technology

1983-01-01

adjusted for each subject to 60 cycles per minute using a metronome. Gait cycle was determined using an electrical pressure switch attached to the...dental burr. Electrodes were filled with conducting gel and held in place with double adhesive rings. An electrical pressure switch was taped to the...the pressure switch was carried on a separate wire to the recording equipment. All wires were held tightly against the subject’s leg to reduce

Transparent electrode for optical switch

DOEpatents

Goldhar, J.; Henesian, M.A.

1984-10-19

The invention relates generally to optical switches and techniques for applying a voltage to an electro-optical crystal, and more particularly, to transparent electodes for an optical switch. System architectures for very large inertial confinement fusion (ICF) lasers require active optical elements with apertures on the order of one meter. Large aperture optical switches are needed for isolation of stages, switch-out from regenerative amplifier cavities and protection from target retroreflections.

Development library of finite elements for computer-aided design system of reed sensors

NASA Astrophysics Data System (ADS)

Kozlov, A. S.; Shmakov, N. A.; Tkalich, V. L.; Labkovskaia, R. I.; Kalinkina, M. E.; Pirozhnikova, O. I.

2018-05-01

The article is devoted to the development of a modern highly reliable element base of devices for security and fire alarm systems, in particular, to the improvement of the quality of contact cores (reed and membrane) of reed sensors. Modeling of elastic sensitive elements uses quadrangular elements of plates and shells, considered in the system of curvilinear orthogonal coordinates. The developed mathematical models and the formed finite element library are designed for systems of automated design of reed switch detectors to create competitive devices alarms. The finite element library is used for the automated system production of reed switch detectors both in series production and in the implementation of individual orders.

Design and evaluation of a DAMQ multiprocessor network with self-compacting buffers

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

Park, J.; O`Krafka, B.W.O.; Vassiliadis, S.

1994-12-31

This paper describes a new approach to implement Dynamically Allocated Multi-Queue (DAMQ) switching elements using a technique called ``self-compacting buffers``. This technique is efficient in that the amount of hardware required to manage the buffers is relatively small; it offers high performance since it is an implementation of a DAMQ. The first part of this paper describes the self-compacting buffer architecture in detail, and compares it against a competing DAMQ switch design. The second part presents extensive simulation results comparing the performance of a self compacting buffer switch against an ideal switch including several examples of k-ary n-cubes and deltamore » networks. In addition, simulation results show how the performance of an entire network can be quickly and accurately approximated by simulating just a single switching element.« less

A Novel Unit Cell for Active Switches in the Millimeter-Wave Frequency Range

NASA Astrophysics Data System (ADS)

Müller, Daniel; Scherer, Gunnar; Lewark, Ulrich J.; Massler, Hermann; Wagner, Sandrine; Tessmann, Axel; Leuther, Arnulf; Zwick, Thomas; Kallfass, Ingmar

2018-02-01

This paper presents a novel transistor unit cell which is intended to realize compact active switches in the high millimeter-wave frequency range. The unit cell consists of the combination of shunt and common gate transistor within a four-finger transistor cell, achieving gain in the amplifying state as well as good isolation in the isolating state. Gate width-dependent characteristics of the unit cell as well as the design of actual switch implementations are discussed in detail. To verify the concept, two switches, a single pole double throw (SPDT) switch and single pole quadruple throw (SP4T) switch, intended for the WR3 frequency range (220-325 GHz) were manufactured and characterized. The measured gain at 250 GHz is 4.6 and 2.2 dB for the SPDT and SP4T switch, respectively. An isolation of more than 24 dB for the SPDT switch and 12.8 dB for the SP4T switch was achieved.

Study of Man-Machine Communications Systems for Disabled Persons (The Handicapped). Volume VII. Final Report.

ERIC Educational Resources Information Center

Kafafian, Haig

Teaching instructions, lesson plans, and exercises are provided for severely physically and/or neurologically handicapped persons learning to use the Cybertype electric writing machine with a tongue-body keyboard. The keyboard, which has eight double-throw toggle switches and a three-position state-selector switch, is designed to be used by…

Series resonance inverter with triggered vacuum gaps

NASA Astrophysics Data System (ADS)

Damstra, Geert C.; Zhang, X.

1994-05-01

Series resonance inverters based on semi-conductor switching elements are well-known and have a wide range of application, mainly for lower voltages. For high voltage application many switching elements have to be put in series to obtain sufficient blocking voltage. Voltage grinding and multiple gate control elements are needed. There is much experience with the triggered vacuum gaps as high voltage/high current single shot elements, for example in reignition circuits for synthetic circuit breaker tests. These elements have a blocking voltage of 50 - 100 kV and are triggerable by a light fiber control device. A prototype inverter has been developed that generates 0.1 Hz, 30 kV AC voltages with a flat top for tests on cables and capacitors of many micro farads fed from a low voltage supply of about 600 V. Only two TVG elements are needed to switch the resonant circuit alternatively on the positive or negative supply. The resonant circuit itself consists of the capacitance of the testobject and a high quality inductor that determines the frequency and the peak current of the voltage reversing process.

Coexistence of bipolar and unipolar resistive switching behaviors in the double-layer Ag/ZnS-Ag/CuAlO2/Pt memory device

NASA Astrophysics Data System (ADS)

Zhang, Lei; Xu, Haiyang; Wang, Zhongqiang; Yu, Hao; Ma, Jiangang; Liu, Yichun

2016-01-01

The coexistence of uniform bipolar and unipolar resistive-switching (RS) characteristics was demonstrated in a double-layer Ag/ZnS-Ag/CuAlO2/Pt memory device. By changing the compliance current (CC) from 1 mA to 10 mA, the RS behavior can be converted from the bipolar mode (BRS) to the unipolar mode (URS). The temperature dependence of low resistance states further indicates that the CFs are composed of the Ag atoms and Cu vacancies for the BRS mode and URS mode, respectively. For this double-layer structure device, the thicker conducting filaments (CFs) will be formed in the ZnS-Ag layer, and it can act as tip electrodes. Thus, the formation and rupture of these two different CFs are located in the CuAlO2 layer, realizing the uniform and stable BRS and URS.

An L-band multi-wavelength Brillouin-erbium fiber laser with switchable frequency spacing

NASA Astrophysics Data System (ADS)

Zhou, Xuefang; Hu, Kongwen; Wei, Yizhen; Bi, Meihua; Yang, Guowei

2017-01-01

In this paper, a novel L-band multi-wavelength Brillouin-erbium fiber laser consisting of two ring cavities is proposed and demonstrated. The frequency spacing can be switched, corresponding to the single and double Brillouin frequency shifts, by toggling the optical switch. Under a 980 nm pump power of 600 mw, and a Brillouin pump power of 4 mW and wavelength of 1599.4 nm, up to 16 Stokes signals with a frequency spacing of 0.089 nm and 5 Stokes signals with double spacing of 0.178 nm are generated. A wavelength tunability of 15 nm (1593 nm  -  1608 nm) is realized for both frequency spacings. The fluctuation of Stokes signals for both single and double Brillouin spacing regimes in the proposed setup is less than 1.5 dB throughout a 30 min time span.

Current-voltage characteristics of double stranded versus single stranded DNA molecules

NASA Astrophysics Data System (ADS)

Hartzell, B.; Chen, Hong; Heremans, J. J.; McCord, B.; Soghomonian, V.

2004-03-01

Investigation of DNA conductivity has focused on the native, duplex structure, with controversial results. Here, we present the influence of the double-helical structure on charge transport through lambda DNA molecules. The current-voltage (I-V) characteristics of both disulfide-labeled double stranded DNA (dsDNA) and disulfide-labeled single stranded DNA (ssDNA) were measured. The ssDNA was formed from the dsDNA using two different methods for comparison purposes: a thermal/chemical denaturation and enzymatic digestion utilizing lambda exonuclease. Resulting I-V characteristics of both the double stranded and single stranded samples were close-to-linear when measured at room temperature. However, the ssDNA samples consistently gave conductivity values about two orders of magnitude smaller in amplitude. Our results suggest an integral relationship between the native structure of DNA with its stacked base pairs and the molecule's ability to support charge transport.(NSF NIRT 0103034)

Isomeric effects on the self-assembly of a plausible prebiotic nucleoside analogue: A theoretical study

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

Vallejo, Emmanuel; Fuentes-Cabrera, Miguel; Sumpter, Bobby G.

For this study, the self-assembly properties of N(9)-(2,3-dihydroxypropyl adenine) (DHPA), a plausible prebiotic nucleoside analogue of adenosine, were investigated using density functional theory. Two different isomers were considered, and it is found that while both isomers can form a variety of structures, including chains, one of them is also able to form cages and helixes. When these results were put in the context of substrate supported molecular self-assembly, it is concluded that gas-phase self-assembly studies that consider isomer identity and composition not only can aid interpreting the experimental results, but also reveal structures that might be overlooked otherwise. In particular,more » this study suggest that a double-helical structure made of DHPA molecules which could have implications in prebiotic chemistry and nanotechnology, is stable even at room temperature. For example electrical properties (energy gap of 4.52eV) and a giant permanent electrical dipole moment (49.22 Debye) were found in our larger double-helical structure (3.7 nm) formed by 14 DHPA molecules. Lastly, the former properties could be convenient for construction of organic dielectric-based devices.« less

Isomeric effects on the self-assembly of a plausible prebiotic nucleoside analogue: A theoretical study

DOE PAGES

Vallejo, Emmanuel; Fuentes-Cabrera, Miguel; Sumpter, Bobby G.; ...

2016-10-22

For this study, the self-assembly properties of N(9)-(2,3-dihydroxypropyl adenine) (DHPA), a plausible prebiotic nucleoside analogue of adenosine, were investigated using density functional theory. Two different isomers were considered, and it is found that while both isomers can form a variety of structures, including chains, one of them is also able to form cages and helixes. When these results were put in the context of substrate supported molecular self-assembly, it is concluded that gas-phase self-assembly studies that consider isomer identity and composition not only can aid interpreting the experimental results, but also reveal structures that might be overlooked otherwise. In particular,more » this study suggest that a double-helical structure made of DHPA molecules which could have implications in prebiotic chemistry and nanotechnology, is stable even at room temperature. For example electrical properties (energy gap of 4.52eV) and a giant permanent electrical dipole moment (49.22 Debye) were found in our larger double-helical structure (3.7 nm) formed by 14 DHPA molecules. Lastly, the former properties could be convenient for construction of organic dielectric-based devices.« less

Estimation of strength in different extra Watson-Crick hydrogen bonds in DNA double helices through quantum chemical studies.

PubMed

Bandyopadhyay, D; Bhattacharyya, D

2006-10-15

It was shown earlier, from database analysis, model building studies, and molecular dynamics simulations that formation of cross-strand bifurcated or Extra Watson-Crick hydrogen (EWC) bonds between successive base pairs may lead to extra rigidity to DNA double helices of certain sequences. The strengths of these hydrogen bonds are debatable, however, as they do not have standard linear geometry criterion. We have therefore carried out detailed ab initio quantum chemical studies using RHF/6-31G(2d,2p) and B3LYP/6-31G(2p,2d) basis sets to determine strengths of several bent hydrogen bonds with different donor and acceptors. Interaction energy calculations, corrected for the basis set superposition errors, suggest that N-H...O type bent EWC hydrogen bonds are possible along same strands or across the strands between successive base pairs, leading to significant stability (ca. 4-9 kcal/mol). The N-H...N and C-H...O type interactions, however, are not so stabilizing. Hence, consideration of EWC N-H...O H-bonds can lead to a better understanding of DNA sequence directed structural features. Copyright (c) 2006 Wiley Periodicals, Inc.

Sikorsky Aircraft Advanced Rotorcraft Transmission (ART) program

NASA Technical Reports Server (NTRS)

Kish, Jules G.

1993-01-01

The objectives of the Advanced Rotorcraft Transmission program were to achieve a 25 percent weight reduction, a 10 dB noise reduction, and a 5,000 hour mean time between removals (MTBR). A three engine Army Cargo Aircraft (ACA) of 85,000 pounds gross weight was used as the baseline. Preliminary designs were conducted of split path and split torque transmissions to evaluate weight, reliability, and noise. A split path gearbox was determined to be 23 percent lighter, greater than 10 dB quieter, and almost four times more reliable than the baseline two stage planetary design. Detail design studies were conducted of the chosen split path configuration, and drawings were produced of a 1/2 size gearbox consisting of a single engine path of the split path section. Fabrication and testing was then conducted on the 1/2 size gearbox. The 1/2 size gearbox testing proved that the concept of the split path gearbox with high reduction ratio double helical output gear was sound. The improvements were attributed to extensive use of composites, spring clutches, advanced high hot hardness gear steels, the split path configuration itself, high reduction ratio, double helical gearing on the output stage, elastomeric load sharing devices, and elimination of accessory drives.

Inclusive cross section and double-helicity asymmetry for $$\\pi^{0}$$ production at midrapidity in $p$$+$$p$ collisions at $$\\sqrt{s}=510$$ GeV

DOE PAGES

Adare, A.

2016-01-07

PHENIX measurements are presented for the cross section and double-helicity asymmetry (ALL) in inclusive π⁰ production at midrapidity from p+p collisions at √s = 510 GeV from data taken in 2012 and 2013 at the Relativistic Heavy Ion Collider. The next-to-leading-order perturbativequantum- chromodynamics theory calculation is in excellent agreement with the presented cross section results. The calculation utilized parton-to-pion fragmentation functions from the recent DSS14 global analysis, which prefer a smaller gluon-to-pion fragmentation function. The π⁰A LL results follow an increasingly positive asymmetry trend with pT and √s with respect to the predictions and are in excellent agreement with themore » latest global analysis results. This analysis incorporated earlier results on π0 and jet A LL, and suggested a positive contribution of gluon polarization to the spin of the proton ΔG for the gluon momentum fraction range x > 0.05. The data presented here extend to a currently unexplored region, down to x 0.01, and thus provide additional constraints on the value of ΔG.« less

Inclusive cross section and double-helicity asymmetry for π0 production at midrapidity in p +p collisions at √{s }=510 GeV

NASA Astrophysics Data System (ADS)

Adare, A.; Aidala, C.; Ajitanand, N. N.; Akiba, Y.; Akimoto, R.; Alexander, J.; Alfred, M.; Aoki, K.; Apadula, N.; Aramaki, Y.; Asano, H.; Atomssa, E. T.; Awes, T. C.; Azmoun, B.; Babintsev, V.; Bai, M.; Bai, X.; Bandara, N. S.; Bannier, B.; Barish, K. N.; Bathe, S.; Baublis, V.; Baumann, C.; Baumgart, S.; Bazilevsky, A.; Beaumier, M.; Beckman, S.; Belmont, R.; Berdnikov, A.; Berdnikov, Y.; Black, D.; Blau, D. S.; Bok, J. S.; Boyle, K.; Brooks, M. L.; Bryslawskyj, J.; Buesching, H.; Bumazhnov, V.; Butsyk, S.; Campbell, S.; Chen, C.-H.; Chi, C. Y.; Chiu, M.; Choi, I. J.; Choi, J. B.; Choi, S.; Christiansen, P.; Chujo, T.; Cianciolo, V.; Citron, Z.; Cole, B. A.; Cronin, N.; Crossette, N.; Csanád, M.; Csörgő, T.; Danley, T. W.; Datta, A.; Daugherity, M. S.; David, G.; Deblasio, K.; Dehmelt, K.; Denisov, A.; Deshpande, A.; Desmond, E. J.; Ding, L.; Dion, A.; Diss, P. B.; Do, J. H.; D'Orazio, L.; Drapier, O.; Drees, A.; Drees, K. A.; Durham, J. M.; Durum, A.; Engelmore, T.; Enokizono, A.; En'yo, H.; Esumi, S.; Eyser, K. O.; Fadem, B.; Feege, N.; Fields, D. E.; Finger, M.; Finger, M.; Fleuret, F.; Fokin, S. L.; Frantz, J. E.; Franz, A.; Frawley, A. D.; Fukao, Y.; Fusayasu, T.; Gainey, K.; Gal, C.; Gallus, P.; Garg, P.; Garishvili, A.; Garishvili, I.; Ge, H.; Giordano, F.; Glenn, A.; Gong, X.; Gonin, M.; Goto, Y.; Granier de Cassagnac, R.; Grau, N.; Greene, S. V.; Grosse Perdekamp, M.; Gu, Y.; Gunji, T.; Guragain, H.; Hachiya, T.; Haggerty, J. S.; Hahn, K. I.; Hamagaki, H.; Hamilton, H. F.; Han, S. Y.; Hanks, J.; Hasegawa, S.; Haseler, T. O. S.; Hashimoto, K.; Hayano, R.; He, X.; Hemmick, T. K.; Hester, T.; Hill, J. C.; Hollis, R. S.; Homma, K.; Hong, B.; Hoshino, T.; Hotvedt, N.; Huang, J.; Huang, S.; Ichihara, T.; Ikeda, Y.; Imai, K.; Imazu, Y.; Inaba, M.; Iordanova, A.; Isenhower, D.; Isinhue, A.; Ivanishchev, D.; Jacak, B. V.; Jeon, S. J.; Jezghani, M.; Jia, J.; Jiang, X.; Johnson, B. M.; Joo, E.; Joo, K. S.; Jouan, D.; Jumper, D. S.; Kamin, J.; Kanda, S.; Kang, B. H.; Kang, J. H.; Kang, J. S.; Kapustinsky, J.; Kawall, D.; Kazantsev, A. V.; Key, J. A.; Khachatryan, V.; Khandai, P. K.; Khanzadeev, A.; Kihara, K.; Kijima, K. M.; Kim, C.; Kim, D. H.; Kim, D. J.; Kim, E.-J.; Kim, G. W.; Kim, H.-J.; Kim, M.; Kim, Y.-J.; Kim, Y. K.; Kimelman, B.; Kistenev, E.; Kitamura, R.; Klatsky, J.; Kleinjan, D.; Kline, P.; Koblesky, T.; Kofarago, M.; Komkov, B.; Koster, J.; Kotchetkov, D.; Kotov, D.; Krizek, F.; Kurita, K.; Kurosawa, M.; Kwon, Y.; Lacey, R.; Lai, Y. S.; Lajoie, J. G.; Lebedev, A.; Lee, D. M.; Lee, G. H.; Lee, J.; Lee, K. B.; Lee, K. S.; Lee, S.; Lee, S. H.; Leitch, M. J.; Leitgab, M.; Lewis, B.; Li, X.; Lim, S. H.; Liu, M. X.; Lynch, D.; Maguire, C. F.; Makdisi, Y. I.; Makek, M.; Manion, A.; Manko, V. I.; Mannel, E.; Maruyama, T.; McCumber, M.; McGaughey, P. L.; McGlinchey, D.; McKinney, C.; Meles, A.; Mendoza, M.; Meredith, B.; Miake, Y.; Mibe, T.; Mignerey, A. C.; Miller, A. J.; Milov, A.; Mishra, D. K.; Mitchell, J. T.; Miyasaka, S.; Mizuno, S.; Mohanty, A. K.; Mohapatra, S.; Montuenga, P.; Moon, T.; Morrison, D. P.; Moskowitz, M.; Moukhanova, T. V.; Murakami, T.; Murata, J.; Mwai, A.; Nagae, T.; Nagamiya, S.; Nagashima, K.; Nagle, J. L.; Nagy, M. I.; Nakagawa, I.; Nakagomi, H.; Nakamiya, Y.; Nakamura, K. R.; Nakamura, T.; Nakano, K.; Nattrass, C.; Netrakanti, P. K.; Nihashi, M.; Niida, T.; Nishimura, S.; Nouicer, R.; Novák, T.; Novitzky, N.; Nyanin, A. S.; O'Brien, E.; Ogilvie, C. A.; Oide, H.; Okada, K.; Orjuela Koop, J. D.; Osborn, J. D.; Oskarsson, A.; Ozaki, H.; Ozawa, K.; Pak, R.; Pantuev, V.; Papavassiliou, V.; Park, I. H.; Park, J. S.; Park, S.; Park, S. K.; Pate, S. F.; Patel, L.; Patel, M.; Peng, J.-C.; Perepelitsa, D. V.; Perera, G. D. N.; Peressounko, D. Yu.; Perry, J.; Petti, R.; Pinkenburg, C.; Pinson, R.; Pisani, R. P.; Purschke, M. L.; Qu, H.; Rak, J.; Ramson, B. J.; Ravinovich, I.; Read, K. F.; Reynolds, D.; Riabov, V.; Riabov, Y.; Richardson, E.; Rinn, T.; Riveli, N.; Roach, D.; Rolnick, S. D.; Rosati, M.; Rowan, Z.; Rubin, J. G.; Ryu, M. S.; Sahlmueller, B.; Saito, N.; Sakaguchi, T.; Sako, H.; Samsonov, V.; Sarsour, M.; Sato, S.; Sawada, S.; Schaefer, B.; Schmoll, B. K.; Sedgwick, K.; Seele, J.; Seidl, R.; Sekiguchi, Y.; Sen, A.; Seto, R.; Sett, P.; Sexton, A.; Sharma, D.; Shaver, A.; Shein, I.; Shibata, T.-A.; Shigaki, K.; Shimomura, M.; Shoji, K.; Shukla, P.; Sickles, A.; Silva, C. L.; Silvermyr, D.; Singh, B. K.; Singh, C. P.; Singh, V.; Skolnik, M.; Slunečka, M.; Snowball, M.; Solano, S.; Soltz, R. A.; Sondheim, W. E.; Sorensen, S. P.; Sourikova, I. V.; Stankus, P. W.; Steinberg, P.; Stenlund, E.; Stepanov, M.; Ster, A.; Stoll, S. P.; Stone, M. R.; Sugitate, T.; Sukhanov, A.; Sumita, T.; Sun, J.; Sziklai, J.; Takahara, A.; Taketani, A.; Tanaka, Y.; Tanida, K.; Tannenbaum, M. J.; Tarafdar, S.; Taranenko, A.; Tennant, E.; Tieulent, R.; Timilsina, A.; Todoroki, T.; Tomášek, M.; Torii, H.; Towell, C. L.; Towell, M.; Towell, R.; Towell, R. S.; Tserruya, I.; van Hecke, H. W.; Vargyas, M.; Vazquez-Zambrano, E.; Veicht, A.; Velkovska, J.; Vértesi, R.; Virius, M.; Vrba, V.; Vznuzdaev, E.; Wang, X. R.; Watanabe, D.; Watanabe, K.; Watanabe, Y.; Watanabe, Y. S.; Wei, F.; Whitaker, S.; White, A. S.; Wolin, S.; Woody, C. L.; Wysocki, M.; Xia, B.; Xue, L.; Yalcin, S.; Yamaguchi, Y. L.; Yanovich, A.; Yokkaichi, S.; Yoo, J. H.; Yoon, I.; You, Z.; Younus, I.; Yu, H.; Yushmanov, I. E.; Zajc, W. A.; Zelenski, A.; Zhou, S.; Zou, L.; Phenix Collaboration

2016-01-01

PHENIX measurements are presented for the cross section and double-helicity asymmetry (AL L ) in inclusive π0 production at midrapidity from p +p collisions at √{s }=510 GeV from data taken in 2012 and 2013 at the Relativistic Heavy Ion Collider. The next-to-leading-order perturbative-quantum-chromodynamics theory calculation is in excellent agreement with the presented cross section results. The calculation utilized parton-to-pion fragmentation functions from the recent DSS14 global analysis, which prefer a smaller gluon-to-pion fragmentation function. The π0AL L results follow an increasingly positive asymmetry trend with pT and √{s } with respect to the predictions and are in excellent agreement with the latest global analysis results. This analysis incorporated earlier results on π0 and jet AL L and suggested a positive contribution of gluon polarization to the spin of the proton Δ G for the gluon momentum fraction range x >0.05 . The data presented here extend to a currently unexplored region, down to x ˜0.01 , and thus provide additional constraints on the value of Δ G .

High-Resolution Free-Energy Landscape Analysis of α-Helical Protein Folding: HP35 and Its Double Mutant

PubMed Central

2013-01-01

The free-energy landscape can provide a quantitative description of folding dynamics, if determined as a function of an optimally chosen reaction coordinate. Here, we construct the optimal coordinate and the associated free-energy profile for all-helical proteins HP35 and its norleucine (Nle/Nle) double mutant, based on realistic equilibrium folding simulations [Piana et al. Proc. Natl. Acad. Sci. U.S.A.2012, 109, 17845]. From the obtained profiles, we directly determine such basic properties of folding dynamics as the configurations of the minima and transition states (TS), the formation of secondary structure and hydrophobic core during the folding process, the value of the pre-exponential factor and its relation to the transition path times, the relation between the autocorrelation times in TS and minima. We also present an investigation of the accuracy of the pre-exponential factor estimation based on the transition-path times. Four different estimations of the pre-exponential factor for both proteins give k0–1 values of approximately a few tens of nanoseconds. Our analysis gives detailed information about folding of the proteins and can serve as a rigorous common language for extensive comparison between experiment and simulation. PMID:24348206

High-Resolution Free-Energy Landscape Analysis of α-Helical Protein Folding: HP35 and Its Double Mutant.

PubMed

Banushkina, Polina V; Krivov, Sergei V

2013-12-10

The free-energy landscape can provide a quantitative description of folding dynamics, if determined as a function of an optimally chosen reaction coordinate. Here, we construct the optimal coordinate and the associated free-energy profile for all-helical proteins HP35 and its norleucine (Nle/Nle) double mutant, based on realistic equilibrium folding simulations [Piana et al. Proc. Natl. Acad. Sci. U.S.A. 2012 , 109 , 17845]. From the obtained profiles, we directly determine such basic properties of folding dynamics as the configurations of the minima and transition states (TS), the formation of secondary structure and hydrophobic core during the folding process, the value of the pre-exponential factor and its relation to the transition path times, the relation between the autocorrelation times in TS and minima. We also present an investigation of the accuracy of the pre-exponential factor estimation based on the transition-path times. Four different estimations of the pre-exponential factor for both proteins give k 0 -1 values of approximately a few tens of nanoseconds. Our analysis gives detailed information about folding of the proteins and can serve as a rigorous common language for extensive comparison between experiment and simulation.

Unsteady numerical analysis of solid-liquid two-phase flow in stirred tank with double helical ribbon impeller

NASA Astrophysics Data System (ADS)

Bai, He; Chen, Xiangshan; Zhao, Guangyu; Xiao, Chenglei; Li, Chen; Zhong, Cheng; Chen, Yu

2017-08-01

In order to enhance the mixing process of soil contaminated by oil and water, one kind of double helical ribbon (DHR) impeller was developed. In this study, the unsteady simulation analysis of solid-liquid two-phase flow in stirring tank with DHR impeller was conducted by the the computational fluid dynamics and the multi-reference frame (MRF) method. It was found that at 0-3.0 s stage, the rate of liquid was greater than the rate of solid particles, while the power consumption was 5-6 times more than the smooth operation. The rates of the liquid and the solid particles were almost the same, and the required power was 32 KW at t > 3.0 s. The flow of the solid particles in the tank was a typical axial circle flow, and the dispersed sequence of the solid that was accumulated at the bottom of the tank was: the bottom loop region, the annular region near the wall of the groove and finally the area near axial center. The results show that the DHR impeller was suitable for the mixing of liquid-solid two-phase.

Comparison between TRF2 and TRF1 of their telomeric DNA-bound structures and DNA-binding activities

PubMed Central

Hanaoka, Shingo; Nagadoi, Aritaka; Nishimura, Yoshifumi

2005-01-01

Mammalian telomeres consist of long tandem arrays of double-stranded telomeric TTAGGG repeats packaged by the telomeric DNA-binding proteins TRF1 and TRF2. Both contain a similar C-terminal Myb domain that mediates sequence-specific binding to telomeric DNA. In a DNA complex of TRF1, only the single Myb-like domain consisting of three helices can bind specifically to double-stranded telomeric DNA. TRF2 also binds to double-stranded telomeric DNA. Although the DNA binding mode of TRF2 is likely identical to that of TRF1, TRF2 plays an important role in the t-loop formation that protects the ends of telomeres. Here, to clarify the details of the double-stranded telomeric DNA-binding modes of TRF1 and TRF2, we determined the solution structure of the DNA-binding domain of human TRF2 bound to telomeric DNA; it consists of three helices, and like TRF1, the third helix recognizes TAGGG sequence in the major groove of DNA with the N-terminal arm locating in the minor groove. However, small but significant differences are observed; in contrast to the minor groove recognition of TRF1, in which an arginine residue recognizes the TT sequence, a lysine residue of TRF2 interacts with the TT part. We examined the telomeric DNA-binding activities of both DNA-binding domains of TRF1 and TRF2 and found that TRF1 binds more strongly than TRF2. Based on the structural differences of both domains, we created several mutants of the DNA-binding domain of TRF2 with stronger binding activities compared to the wild-type TRF2. PMID:15608118

Fabrication of micro- and nanometre-scale polymer structures in liquid crystal devices for next generation photonics applications

NASA Astrophysics Data System (ADS)

Tartan, Chloe C.; Salter, Patrick S.; Booth, Martin J.; Morris, Stephen M.; Elston, Steve J.

2016-09-01

Direct Laser Writing (DLW) by two-photon photopolymerization (TPP) enables the fabrication of micron-scale polymeric structures in soft matter systems. The technique has implications in a broad range of optics and photonics; in particular fast-switching liquid crystal (LC) modes for the development of next generation display technologies. In this paper, we report two different methodologies using our TPP-based fabrication technique. Two explicit examples are provided of voltage-dependent LC director profiles that are inherently unstable, but which appear to be promising candidates for fast-switching photonics applications. In the first instance, 1 μm-thick periodic walls of polymer network are written into a planar aligned (parallel rubbed) nematic pi-cell device containing a nematic LC-monomer mixture. The structures are fabricated when the device is electrically driven into a fast-switching nematic LC state and aberrations induced by the device substrates are corrected for by virtue of the adaptive optics elements included within the DLW setup. Optical polarizing microscopy images taken post-fabrication reveal that polymer walls oriented perpendicular to the rubbing direction promote the stability of the so-called optically compensated bend mode upon removal of the externally applied field. In the second case, polymer walls are written in a nematic LC-optically adhesive glue mixture. A polymer- LCs-polymer-slices or `POLICRYPS' template is formed by immersing the device in acetone post-fabrication to remove any remaining non-crosslinked material. Injecting the resultant series of polymer microchannels ( 1 μm-thick) with a short-pitch, chiral nematic LC mixture leads to the spontaneous alignment of a fast-switching chiral nematic mode, where the helical axis lies parallel to the glass substrates. Optimal contrast between the bright and dark states of the uniform lying helix alignment is achieved when the structures are spaced at the order of the device thickness, which was also found to be the case for the achiral system. The high resolution DLW technique limits structures to the focal spot size of the beam, 1 μm in diameter, such that the transmittance is expected to be significantly enhanced relative to other stabilization techniques. Moreover, both devices remain stable under electrical and thermal cycling.

From Mesocates to Helicates: Structural, Magnetic and Chiro-Optical Studies on Nickel(II) Supramolecular Assemblies Derived from Tetradentate Schiff Bases.

PubMed

Mayans, Júlia; Font-Bardia, Mercè; Di Bari, Lorenzo; Arrico, Lorenzo; Zinna, Francesco; Pescitelli, Gennaro; Escuer, Albert

2018-05-28

The systematic reactions of a family of tetradentate pyridyl/imine and quinolyl/imine racemic or enantiopure Schiff bases with Ni(NO 3 ) 2 or Ni(ClO 4 ) 2 in the presence of sodium azide yielded, as a function of the starting racemic, chiral or achiral base, a set of chiral, meso or achiral complexes. In all cases, the compounds consist of two Ni II cations linked by a double azido bridge in its end-on coordination mode. All the dimers exhibit a mesocate supramolecular structure and one of them, the unprecedented mix of helicate and mesocate in 2:1 ratio. The transition from mesocate to helicate conformation has been reached by tuning the flexibility of the central spacers of the Schiff bases and the size of the substituents. Electronic circular dichroism (ECD) studies have been performed for two pairs of enantiomers and interpreted by means of DFT calculations. Susceptibility measurements show a ferromagnetic coupling between the Ni II cations mediated by the end-on azido bridges. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Conductance and amantadine binding of a pore formed by a lysine-flanked transmembrane domain of SARS coronavirus envelope protein

PubMed Central

Torres, Jaume; Maheswari, Uma; Parthasarathy, Krupakar; Ng, Lifang; Liu, Ding Xiang; Gong, Xiandi

2007-01-01

The coronavirus responsible for the severe acute respiratory syndrome (SARS-CoV) contains a small envelope protein, E, with putative involvement in host cell apoptosis and virus morphogenesis. It has been suggested that E protein can form a membrane destabilizing transmembrane (TM) hairpin, or homooligomerize to form a regular TM α-helical bundle. We have shown previously that the topology of the α-helical putative TM domain of E protein (ETM), flanked by two lysine residues at C and N termini to improve solubility, is consistent with a regular TM α-helix, with orientational parameters in lipid bilayers that are consistent with a homopentameric model. Herein, we show that this peptide, reconstituted in lipid bilayers, shows sodium conductance. Channel activity is inhibited by the anti-influenza drug amantadine, which was found to bind our preparation with moderate affinity. Results obtained from single or double mutants indicate that the organization of the transmembrane pore is consistent with our previously reported pentameric α-helical bundle model. PMID:17766393

Polymorphism complexity and handedness inversion in serum albumin amyloid fibrils.

PubMed

Usov, Ivan; Adamcik, Jozef; Mezzenga, Raffaele

2013-12-23

Protein-based amyloid fibrils can show a great variety of polymorphic structures within the same protein precursor, although the origins of these structural homologues remain poorly understood. In this work we investigate the fibrillation of bovine serum albumin--a model globular protein--and we follow the polymorphic evolution by a statistical analysis of high-resolution atomic force microscopy images, complemented, at larger length scales, by concepts based on polymer physics formalism. We identify six distinct classes of coexisting amyloid fibrils, including flexible left-handed twisted ribbons, rigid right-handed helical ribbons and nanotubes. We show that the rigid fibrils originate from flexible fibrils through two diverse polymorphic transitions, first, via a single-fibril transformation when the flexible left-handed twisted ribbons turn into the helical left-handed ribbons, to finally evolve into nanotube-like structures, and second, via a double-fibril transformation when two flexible left-handed twisted ribbons wind together resulting in a right-handed twisted ribbon, followed by a rigid right-handed helical ribbon polymorphic conformation. Hence, the change in handedness occurs with an increase in the level of the fibril's structural organization.

Task Switching in a Hierarchical Task Structure: Evidence for the Fragility of the Task Repetition Benefit

ERIC Educational Resources Information Center

Lien, Mei-Ching; Ruthruff, Eric

2004-01-01

This study examined how task switching is affected by hierarchical task organization. Traditional task-switching studies, which use a constant temporal and spatial distance between each task element (defined as a stimulus requiring a response), promote a flat task structure. Using this approach, Experiment 1 revealed a large switch cost of 238 ms.…

Structural Study of the RIPoptosome Core Reveals a Helical Assembly for Kinase Recruitment

PubMed Central

2015-01-01

Receptor interaction protein kinase 1 (RIP1) is a molecular cell-fate switch. RIP1, together with Fas-associated protein with death domain (FADD) and caspase-8, forms the RIPoptosome that activates apoptosis. RIP1 also associates with RIP3 to form the necrosome that triggers necroptosis. The RIPoptosome assembles through interactions between the death domains (DDs) of RIP1 and FADD and between death effector domains (DEDs) of FADD and caspase-8. In this study, we analyzed the overall structure of the RIP1 DD/FADD DD complex, the core of the RIPoptosome, by negative-stain electron microscopy and modeling. The results show that RIP1 DD and FADD DD form a stable complex in vitro similar to the previously described Fas DD/FADD DD complex, suggesting that the RIPoptosome and the Fas death-inducing signaling complex share a common assembly mechanism. Both complexes adopt a helical conformation that requires type I, II, and III interactions between the death domains. PMID:25119434

Strong-field approximation in a rotating frame: High-order harmonic emission from p states in bicircular fields

NASA Astrophysics Data System (ADS)

Pisanty, Emilio; Jiménez-Galán, Álvaro

2017-12-01

High-order harmonic generation with bicircular fields—the combination of counter-rotating circularly polarized pulses at different frequencies—results in a series of short-wavelength XUV harmonics with alternating circular polarizations, and experiments show that there is an asymmetry in the emission between the two helicities: a slight one in helium and a larger one in neon and argon, where the emission is carried out by p -shell electrons. Here we analyze this asymmetry by switching to a rotating frame in which the field is linearly polarized; this induces an effective magnetic field which lowers the ionization potential of the p + orbital that corotates with the lower-frequency driver, enhancing its harmonic emission and the overall helicity of the generated harmonics, while also introducing nontrivial effects from the transformation to a noninertial frame in complex time. In addition, this analysis directly relates the small asymmetry produced by s -shell emission to the imaginary part of the recollision velocity in the standard strong-field-approximation formalism.

Design of a minimal protein oligomerization domain by a structural approach.

PubMed

Burkhard, P; Meier, M; Lustig, A

2000-12-01

Because of the simplicity and regularity of the alpha-helical coiled coil relative to other structural motifs, it can be conveniently used to clarify the molecular interactions responsible for protein folding and stability. Here we describe the de novo design and characterization of a two heptad-repeat peptide stabilized by a complex network of inter- and intrahelical salt bridges. Circular dichroism spectroscopy and analytical ultracentrifugation show that this peptide is highly alpha-helical and 100% dimeric tinder physiological buffer conditions. Interestingly, the peptide was shown to switch its oligomerization state from a dimer to a trimer upon increasing ionic strength. The correctness of the rational design principles used here is supported by details of the atomic structure of the peptide deduced from X-ray crystallography. The structure of the peptide shows that it is not a molten globule but assumes a unique, native-like conformation. This de novo peptide thus represents an attractive model system for the design of a molecular recognition system.

Design of a minimal protein oligomerization domain by a structural approach.

PubMed Central

Burkhard, P.; Meier, M.; Lustig, A.

2000-01-01

Because of the simplicity and regularity of the alpha-helical coiled coil relative to other structural motifs, it can be conveniently used to clarify the molecular interactions responsible for protein folding and stability. Here we describe the de novo design and characterization of a two heptad-repeat peptide stabilized by a complex network of inter- and intrahelical salt bridges. Circular dichroism spectroscopy and analytical ultracentrifugation show that this peptide is highly alpha-helical and 100% dimeric tinder physiological buffer conditions. Interestingly, the peptide was shown to switch its oligomerization state from a dimer to a trimer upon increasing ionic strength. The correctness of the rational design principles used here is supported by details of the atomic structure of the peptide deduced from X-ray crystallography. The structure of the peptide shows that it is not a molten globule but assumes a unique, native-like conformation. This de novo peptide thus represents an attractive model system for the design of a molecular recognition system. PMID:11206050

Lasing in a three-dimensional photonic crystal of the liquid crystal blue phase II.

PubMed

Cao, Wenyi; Muñoz, Antonio; Palffy-Muhoray, Peter; Taheri, Bahman

2002-10-01

Photonic-bandgap materials, with periodicity in one, two or three dimensions, offer control of spontaneous emission and photon localization. Low-threshold lasing has been demonstrated in two-dimensional photonic-bandgap materials, both with distributed feedback and defect modes. Liquid crystals with chiral constituents exhibit mesophases with modulated ground states. Helical cholesterics are one-dimensional, whereas blue phases are three-dimensional self-assembled photonic-bandgap structures. Although mirrorless lasing was predicted and observed in one-dimensional helical cholesteric materials and chiral ferroelectric smectic materials, it is of great interest to probe light confinement in three dimensions. Here, we report the first observations of lasing in three-dimensional photonic crystals, in the cholesteric blue phase II. Our results show that distributed feedback is realized in three dimensions, resulting in almost diffraction-limited lasing with significantly lower thresholds than in one dimension. In addition to mirrorless lasing, these self-assembled soft photonic-bandgap materials may also be useful for waveguiding, switching and sensing applications.

Multi-region relaxed magnetohydrodynamics in plasmas with slowly changing boundaries -- Resonant response of a plasma slab

DOE PAGES

Dewar, R. L.; Hudson, S. R.; Bhattacharjee, A.; ...

2017-04-03

The adiabatic limit of a recently proposed dynamical extension of Taylor relaxation, multi-region relaxed magnetohydrodynamics (MRxMHD), is summarized, with special attention to the appropriate definition of a relative magnetic helicity. The formalism is illustrated using a simple two-region, sheared-magnetic-field model similar to the Hahm-Kulsrud-Taylor (HKT) rippled-boundary slab model. In MRxMHD, a linear Grad-Shafranov equation applies, even at finite ripple amplitude. The adiabatic switching on of boundary ripple excites a shielding current sheet opposing reconnection at a resonant surface. The perturbed magnetic field as a function of ripple amplitude is calculated by invoking the conservation of magnetic helicity in the twomore » regions separated by the current sheet. Here, at low ripple amplitude, "half islands" appear on each side of the current sheet, locking the rotational transform at the resonant value. Beyond a critical amplitude, these islands disappear and the rotational transform develops a discontinuity across the current sheet. Published by AIP Publishing.« less

Multi-region relaxed magnetohydrodynamics in plasmas with slowly changing boundaries -- Resonant response of a plasma slab

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

Dewar, R. L.; Hudson, S. R.; Bhattacharjee, A.

The adiabatic limit of a recently proposed dynamical extension of Taylor relaxation, multi-region relaxed magnetohydrodynamics (MRxMHD), is summarized, with special attention to the appropriate definition of a relative magnetic helicity. The formalism is illustrated using a simple two-region, sheared-magnetic-field model similar to the Hahm-Kulsrud-Taylor (HKT) rippled-boundary slab model. In MRxMHD, a linear Grad-Shafranov equation applies, even at finite ripple amplitude. The adiabatic switching on of boundary ripple excites a shielding current sheet opposing reconnection at a resonant surface. The perturbed magnetic field as a function of ripple amplitude is calculated by invoking the conservation of magnetic helicity in the twomore » regions separated by the current sheet. Here, at low ripple amplitude, "half islands" appear on each side of the current sheet, locking the rotational transform at the resonant value. Beyond a critical amplitude, these islands disappear and the rotational transform develops a discontinuity across the current sheet. Published by AIP Publishing.« less

Ultrafast optomechanical pulse picking

NASA Astrophysics Data System (ADS)

Lilienfein, Nikolai; Holzberger, Simon; Pupeza, Ioachim

2017-01-01

State-of-the-art optical switches for coupling pulses into and/or out of resonators are based on either the electro-optic or the acousto-optic effect in transmissive elements. In high-power applications, the damage threshold and other nonlinear and thermal effects in these elements impede further improvements in pulse energy, duration, and average power. We propose a new optomechanical switching concept which is based solely on reflective elements and is suitable for switching times down to the ten-nanosecond range. To this end, an isolated section of a beam path is moved in a system comprising mirrors rotating at a high angular velocity and stationary imaging mirrors, without affecting the propagation of the beam thereafter. We discuss three variants of the concept and exemplify practical parameters for its application in regenerative amplifiers and stack-and-dump enhancement cavities. We find that optomechanical pulse picking has the potential to achieve switching rates of up to a few tens of kilohertz while supporting pulse energies of up to several joules.

Action of molecular switches in GPCRs--theoretical and experimental studies.

PubMed

Trzaskowski, B; Latek, D; Yuan, S; Ghoshdastider, U; Debinski, A; Filipek, S

2012-01-01

G protein coupled receptors (GPCRs), also called 7TM receptors, form a huge superfamily of membrane proteins that, upon activation by extracellular agonists, pass the signal to the cell interior. Ligands can bind either to extracellular N-terminus and loops (e.g. glutamate receptors) or to the binding site within transmembrane helices (Rhodopsin-like family). They are all activated by agonists although a spontaneous auto-activation of an empty receptor can also be observed. Biochemical and crystallographic methods together with molecular dynamics simulations and other theoretical techniques provided models of the receptor activation based on the action of so-called "molecular switches" buried in the receptor structure. They are changed by agonists but also by inverse agonists evoking an ensemble of activation states leading toward different activation pathways. Switches discovered so far include the ionic lock switch, the 3-7 lock switch, the tyrosine toggle switch linked with the nPxxy motif in TM7, and the transmission switch. The latter one was proposed instead of the tryptophan rotamer toggle switch because no change of the rotamer was observed in structures of activated receptors. The global toggle switch suggested earlier consisting of a vertical rigid motion of TM6, seems also to be implausible based on the recent crystal structures of GPCRs with agonists. Theoretical and experimental methods (crystallography, NMR, specific spectroscopic methods like FRET/BRET but also single-molecule-force-spectroscopy) are currently used to study the effect of ligands on the receptor structure, location of stable structural segments/domains of GPCRs, and to answer the still open question on how ligands are binding: either via ensemble of conformational receptor states or rather via induced fit mechanisms. On the other hand the structural investigations of homoand heterodimers and higher oligomers revealed the mechanism of allosteric signal transmission and receptor activation that could lead to design highly effective and selective allosteric or ago-allosteric drugs.

Electronic devices containing switchably conductive silicon oxides as a switching element and methods for production and use thereof

DOEpatents

Tour, James M.; Yao, Jun; Natelson, Douglas; Zhong, Lin; He, Tao

2015-09-08

In various embodiments, electronic devices containing switchably conductive silicon oxide as a switching element are described herein. The electronic devices are two-terminal devices containing a first electrical contact and a second electrical contact in which at least one of the first electrical contact or the second electrical contact is deposed on a substrate to define a gap region therebetween. A switching layer containing a switchably conductive silicon oxide resides in the gap region between the first electrical contact and the second electrical contact. The electronic devices exhibit hysteretic current versus voltage properties, enabling their use in switching and memory applications. Methods for configuring, operating and constructing the electronic devices are also presented herein.

Electronic devices containing switchably conductive silicon oxides as a switching element and methods for production and use thereof

DOEpatents

Tour, James M; Yao, Jun; Natelson, Douglas; Zhong, Lin; He, Tao

2013-11-26

In various embodiments, electronic devices containing switchably conductive silicon oxide as a switching element are described herein. The electronic devices are two-terminal devices containing a first electrical contact and a second electrical contact in which at least one of the first electrical contact or the second electrical contact is deposed on a substrate to define a gap region therebetween. A switching layer containing a switchably conductive silicon oxide resides in the the gap region between the first electical contact and the second electrical contact. The electronic devices exhibit hysteretic current versus voltage properties, enabling their use in switching and memory applications. Methods for configuring, operating and constructing the electronic devices are also presented herein.

Double quick, double click reversible peptide “stapling”† †Electronic supplementary information (ESI) available: Synthesis and characterization, additional biophysical and biochemical analyses. See DOI: 10.1039/c7sc01342f Click here for additional data file. Click here for additional data file. Click here for additional data file.

PubMed Central

Grison, Claire M.; Burslem, George M.; Miles, Jennifer A.; Pilsl, Ludwig K. A.; Yeo, David J.; Imani, Zeynab; Warriner, Stuart L.; Webb, Michael E.

2017-01-01

The development of constrained peptides for inhibition of protein–protein interactions is an emerging strategy in chemical biology and drug discovery. This manuscript introduces a versatile, rapid and reversible approach to constrain peptides in a bioactive helical conformation using BID and RNase S peptides as models. Dibromomaleimide is used to constrain BID and RNase S peptide sequence variants bearing cysteine (Cys) or homocysteine (hCys) amino acids spaced at i and i + 4 positions by double substitution. The constraint can be readily removed by displacement of the maleimide using excess thiol. This new constraining methodology results in enhanced α-helical conformation (BID and RNase S peptide) as demonstrated by circular dichroism and molecular dynamics simulations, resistance to proteolysis (BID) as demonstrated by trypsin proteolysis experiments and retained or enhanced potency of inhibition for Bcl-2 family protein–protein interactions (BID), or greater capability to restore the hydrolytic activity of the RNAse S protein (RNase S peptide). Finally, use of a dibromomaleimide functionalized with an alkyne permits further divergent functionalization through alkyne–azide cycloaddition chemistry on the constrained peptide with fluorescein, oligoethylene glycol or biotin groups to facilitate biophysical and cellular analyses. Hence this methodology may extend the scope and accessibility of peptide stapling. PMID:28970902

Comparative assessment of the efficacy of closed helical loop and T-loop for space closure in lingual orthodontics-a finite element study.

PubMed

Chacko, Ajay; Tikku, Tripti; Khanna, Rohit; Maurya, Rana Pratap; Srivastava, Kamna

2018-05-28

Retraction in lingual orthodontics has biomechanical differences when compared to labial orthodontics, which is not yet established. Thus, we have intended to compare the biomechanical characteristics of closed helical loop and T-loop on 1 mm activation with 30° of compensatory curvatures during retraction in lingual orthodontics. STb lingual brackets were indirectly bonded to maxillary typhodont model that was scanned to obtain FEM model. Closed helical loop (2 × 7 mm) and T-loop (6 × 2 × 7 mm) of 0.016″ × 0.016″ TMA wire were modeled without preactivation bends. Preactivation bends at 30° were given in the software. Boundary conditions were set. The force (F) and moment (M) of both the loops were determined on 1 mm activation, using ANSYS software. M/F ratio was also calculated for both the loops. T-loop exerted less force, thus increased M/F ratio as compared to closed helical loop on 1 mm activation. When torque has to be preserved in the anterior segment during retraction in lingual orthodontics, T-loop can be preferred over closed helical loop.

The monomeric, tetrameric, and fibrillar organization of Fib: the dynamic building block of the bacterial linear motor of Spiroplasma melliferum BC3.

PubMed

Cohen-Krausz, Sara; Cabahug, Pamela C; Trachtenberg, Shlomo

2011-07-08

Spiroplasmas belong to the class Mollicutes, representing the minimal, free-living, and self-replicating forms of life. Spiroplasmas are helical wall-less bacteria and the only ones known to swim by means of a linear motor (rather than the near-universal rotary bacterial motor). The linear motor follows the shortest path along the cell's helical membranal tube. The motor is composed of a flat monolayered ribbon of seven parallel fibrils and is believed to function in controlling cell helicity and motility through dynamic, coordinated, differential length changes in the fibrils. The latter cause local perturbations of helical symmetry, which are essential for net directional displacement in environments with a low Reynolds number. The underlying fibrils' core building block is a circular tetramer of the 59-kDa protein Fib. The fibrils' differential length changes are believed to be driven by molecular switching of Fib, leading consequently to axial ratio and length changes in tetrameric rings. Using cryo electron microscopy, diffractometry, single-particle analysis of isolated ribbons, and sequence analyses of Fib, we determined the overall molecular organization of the Fib monomer, tetramer, fibril, and linear motor of Spiroplasma melliferum BC3 that underlies cell geometry and motility. Fib appears to be a bidomained molecule, of which the N-terminal half is apparently a globular phosphorylase. By a combination of reversible rotation and diagonal shift of Fib monomers, the tetramer adopts either a cross-like nonhanded conformation or a ring-like handed conformation. The sense of Fib rotation may determine the handedness of the linear motor and, eventually, of the cell. A further change in the axial ratio of the ring-like tetramers controls fibril lengths and the consequent helical geometry. Analysis of tetramer quadrants from adjacent fibrils clearly demonstrates local differential fibril lengths. Copyright © 2011 Elsevier Ltd. All rights reserved.

MEMS for optical switching: technologies, applications, and perspectives

NASA Astrophysics Data System (ADS)

Lin, Lih-Y.; Goldstein, Evan L.

1999-09-01

Micro-electro-mechanical-systems (MEMS), due to their unique ability to integrate electrical, mechanical, and optical elements on a single chip, have recently begun to exhibit great potential for realizing optical components and subsystems in compact, lowcost form. Recently, this technology has been applied to wavelength-division-multiplexed (WDM) networks, and resulted in advances in several network elements, including switches, filters, modulators, and wavelength-add/drop multiplexers. Due largely to the exploding capacity demand arising from data traffic, the transmission capacity demanded of and available from WDM networks is anticipated to increase rapidly. For managing such networks, optical switching is of particular interest due to the fact that its complexity is essentially immune to steady advances in the per-channel bit-rate. We will review various micromachined optical-switching technologies, emphasizing studies of their reliability. We then summarizing recent progress in the free-space MEMS optical switch we have demonstrated.

MEMS for optical switching: technologies, applications, and perspectives

NASA Astrophysics Data System (ADS)

Lin, Lih-Yuan; Goldstein, Evan L.

1999-09-01

Micro-electro-mechanical-systems (MEMS), due to their unique ability to integrate electrical, mechanical, and optical elements on a single chip, have recently begun to exhibit great potential for realizing optical components and subsystems in compact, low-cost form. Recently, this technology has been applied to wavelength-division-multiplexed (WDM) networks, and resulted in advances in several network elements, including switches, filters, modulators, and wavelength-add/drop multiplexers. Due largely to the exploding capacity demand arising from data traffic, the transmission capacity demanded of and available from WDM networks is anticipated to increase rapidly. For managing such networks, optical switching is of particular interest due to the fact that its complexity is essentially immune to steady advances in the per-channel bit-rate. We will review various micromachined optical-switching technologies, emphasizing studies of their reliability. We then summarizing recent progress in the free-space MEMS optical switch we have demonstrated.

Nucleic acid duplexes incorporating a dissociable covalent base pair

PubMed Central

Gao, Kui; Orgel, Leslie E.

1999-01-01

We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure. PMID:10611299

Lack of ubiquitin immunoreactivities at both ends of neuropil threads. Possible bidirectional growth of neuropil threads.

PubMed Central

Iwatsubo, T.; Hasegawa, M.; Esaki, Y.; Ihara, Y.

1992-01-01

Immunocytochemically, neuropil threads (curly fibers) were investigated in the Alzheimer's disease brain using a confocal laser scanning fluorescence microscope by double labeling with tau/ubiquitin antibodies. Ubiquitin immunoreactivities were found to be lacking at one or both ends in more than 40% of tau-positive threads. Immunoelectron microscopy showed that bundles of paired helical filaments, which constitute neuropil threads, were positive for ubiquitin around their midportions, but often negative at their ends. Since it is reasonable to postulate that tau deposition as paired helical filaments precedes ubiquitination, the aforementioned observation suggests that the ends of the threads are newly formed portions, and thus the threads are often growing bidirectionally in small neuronal processes. Images Figure 1 Figure 2 PMID:1310831

Synthesis and Properties of Size-expanded DNAs: Toward Designed, Functional Genetic Systems

PubMed Central

Krueger, Andrew T.; Lu, Haige; Lee, Alex H. F.; Kool, Eric T.

2008-01-01

We describe the design, synthesis, and properties of DNA-like molecules in which the base pairs are expanded by benzo homologation. The resulting size-expanded genetic helices are called xDNA (“expanded DNA”) and yDNA (“wide DNA”). The large component bases are fluorescent, and they display high stacking affinity. When singly substituted into natural DNA, they are destabilizing because the benzo-expanded base pair size is too large for the natural helix. However, when all base pairs are expanded, xDNA and yDNA form highly stable, sequence-selective double helices. The size-expanded DNAs are candidates for components of new, functioning genetic systems. In addition, the fluorescence of expanded DNA bases makes them potentially useful in probing nucleic acids. PMID:17309194

Structure of the starch granule--a curved crystal.

PubMed

Larsson, K

1991-09-01

A structure model of the molecular arrangement in native starch proposed earlier is further considered, with special regard to the lateral packing of cluster units. The amylopectin molecules are radially distributed, with branches concentrated in clusters. Within each cluster the polyglucan chains form double helices which are hexagonally packed. The clusters form spherically concentric crystalline layers with amylose in an amorphous form acting as a space-filler. A translational mechanism for the change of helical direction at boundaries between clusters is proposed which can account for variations in the curvature of the concentric layers. The model is related to X-ray diffraction data and optical birefringence, considering dissembly at gelatinization. The structure is also discussed in relation to biosynthesis. Some aspects of gelatinization, such as the recent glass-transition approach, are then considered.

Predicting RNA pseudoknot folding thermodynamics

PubMed Central

Cao, Song; Chen, Shi-Jie

2006-01-01

Based on the experimentally determined atomic coordinates for RNA helices and the self-avoiding walks of the P (phosphate) and C4 (carbon) atoms in the diamond lattice for the polynucleotide loop conformations, we derive a set of conformational entropy parameters for RNA pseudoknots. Based on the entropy parameters, we develop a folding thermodynamics model that enables us to compute the sequence-specific RNA pseudoknot folding free energy landscape and thermodynamics. The model is validated through extensive experimental tests both for the native structures and for the folding thermodynamics. The model predicts strong sequence-dependent helix-loop competitions in the pseudoknot stability and the resultant conformational switches between different hairpin and pseudoknot structures. For instance, for the pseudoknot domain of human telomerase RNA, a native-like and a misfolded hairpin intermediates are found to coexist on the (equilibrium) folding pathways, and the interplay between the stabilities of these intermediates causes the conformational switch that may underlie a human telomerase disease. PMID:16709732

Molecular-channel driven actuator with considerations for multiple configurations and color switching.

PubMed

Mu, Jiuke; Wang, Gang; Yan, Hongping; Li, Huayu; Wang, Xuemin; Gao, Enlai; Hou, Chengyi; Pham, Anh Thi Cam; Wu, Lianjun; Zhang, Qinghong; Li, Yaogang; Xu, Zhiping; Guo, Yang; Reichmanis, Elsa; Wang, Hongzhi; Zhu, Meifang

2018-02-09

The ability to achieve simultaneous intrinsic deformation with fast response in commercially available materials that can safely contact skin continues to be an unresolved challenge for artificial actuating materials. Rather than using a microporous structure, here we show an ambient-driven actuator that takes advantage of inherent nanoscale molecular channels within a commercial perfluorosulfonic acid ionomer (PFSA) film, fabricated by simple solution processing to realize a rapid response, self-adaptive, and exceptionally stable actuation. Selective patterning of PFSA films on an inert soft substrate (polyethylene terephthalate film) facilitates the formation of a range of different geometries, including a 2D (two-dimensional) roll or 3D (three-dimensional) helical structure in response to vapor stimuli. Chemical modification of the surface allowed the development of a kirigami-inspired single-layer actuator for personal humidity and heat management through macroscale geometric design features, to afford a bilayer stimuli-responsive actuator with multicolor switching capability.

Entropy Generation Analysis through Helical Coil Heat Exchanger in an Agitated Vessel

NASA Astrophysics Data System (ADS)

Ashok Reddy, K.

2018-03-01

Entropy Generation have been obtained while conducting the experiments for different sodium carboxymethyl cellulose concentrations 0.05%,0.1%,0.15% and 0.2% of Newtonian and non Newtonian fluids and the data made available by passing the test fluid at different flow rates through a helical coil in a mixing coil using paddle impeller. Heating of fluids depend on operational parameters, geometry of the mixing vessel and the type of impeller used. A new design of heating element was design and fabricated by providing kanthal wire inserted into a glove knitted with fiber glass yarn as glass fabric is flexible, heat resistant and can accommodate to adopt small difference in size of the vessel, perfectly. The knitted fabric is made to the shape of vessel used in the experiment and the heating elements are inserted so that it gets embedded and forms part of the glove knitted with yarn of fiber glass.

Tuning the metamagnetism in a metallic helical antiferromagnet

NASA Astrophysics Data System (ADS)

Ma, S. C.; Liu, K.; Ma, C. C.; Ge, Q.; Zhang, J. T.; Hu, Y. F.; Liu, E. K.; Zhong, Z. C.

2017-12-01

The antiferromagnetic (AFM)-ferromagnetic (FM) conversion in martensite was observed in Mn/Ni-substitution upon FM elements, such as Fe or Co, in MnNiGe helical antiferromagnets. Here, we report an AFM-FM conversion and consequently a sharp magnetic-field-driven metamagnetic martensitic transformation from paramagnetic (PM) austenite to FM martensite in the Ni- and Mn-substituted MnNiGe alloys with indium, a non-magnetic and large-sized main group element. Accordingly, a giant magnetocaloric effect such that a twofold increase of the magnetic entropy change in MnNi0.92GeIn0.08 and even a nearly threefold increase in the Mn0.92NiGeIn0.08 alloy is obtained with respect to the MnNiGe0.95In0.05 alloy. The origin of AFM-FM conversion and resultantly sharp magnetic-field-induced PM-FM metamagnetic transformation is discussed based on the first-principles calculations and X-ray absorption spectroscopic results.

Shape morphing and motion of responsive hydrogel composites

NASA Astrophysics Data System (ADS)

Hayward, Ryan

Composites of stimuli-responsive hydrogels paired with stiff structural elements or functional inorganic materials offer myriad opportunities to control the shape, properties, and motion of materials. In one example, our group has studied the geometry and mechanics of swelling-induced buckling of polymer trilayer films consisting of patterning rigid layers sandwiching a swellable hydrogel layer. Of particular recent interest has been the formation of helical structures from seedpod-type architectures with perpendicular orientation of stripes on opposite faces. We have studied the concatenation of two or more helical segments, yielding simple geometric design rules for the fabrication of 3D constructs. In a second example, we have considered the light-driven reshaping and motion of hydrogels containing plasmonic nanoparticles as photothermal heating elements. In contrast to systems pre-programmed to take on a single, or perhaps a few, different 3D shapes, this approach enables continuous shape reconfiguration, and correspondingly, directed motion of composite hydrogel sheets.

An Organic Vortex Laser.

PubMed

Stellinga, Daan; Pietrzyk, Monika E; Glackin, James M E; Wang, Yue; Bansal, Ashu K; Turnbull, Graham A; Dholakia, Kishan; Samuel, Ifor D W; Krauss, Thomas F

2018-03-27

Optical vortex beams are at the heart of a number of novel research directions, both as carriers of information and for the investigation of optical activity and chiral molecules. Optical vortex beams are beams of light with a helical wavefront and associated orbital angular momentum. They are typically generated using bulk optics methods or by a passive element such as a forked grating or a metasurface to imprint the required phase distribution onto an incident beam. Since many applications benefit from further miniaturization, a more integrated yet scalable method is highly desirable. Here, we demonstrate the generation of an azimuthally polarized vortex beam directly by an organic semiconductor laser that meets these requirements. The organic vortex laser uses a spiral grating as a feedback element that gives control over phase, handedness, and degree of helicity of the emitted beam. We demonstrate vortex beams up to an azimuthal index l = 3 that can be readily multiplexed into an array configuration.

Air-bridge and Vertical CNT Switches for High Performance Switching Applications

NASA Technical Reports Server (NTRS)

Kaul, Anupama B.; Wong, Eric W.; Epp, Larry; Bronikowski, Michael J.; Hunt, BBrian D.

2006-01-01

Carbon nanotubes are attractive for switching applications since electrostatically-actuated CNT switches have low actuation voltages and power requirements, while allowing GHz switching speeds that stem from the inherently high elastic modulus and low mass of the CNT.Our first NEM structure, the air-bridge switch, consists of suspended single-walled nanotubes (SWNTs) that lie above a sputtered Nb base electrode, where contact to the CNTs is made using evaporated Au/Ti. Electrical measurements of these air-bridge devices show well-defined ON and OFF states as a dc bias of a few volts is applied between the CNT and the Nb-base electrode. The CNT air-bridge switches were measured to have switching times down to a few nanoseconds. Our second NEM structure, the vertical CNT switch, consists of nanotubes grown perpendicular to the substrate. Vertical multi-walled nanotubes (MWNTs) are grown directly on a heavily doped Si substrate, from 200 - 300 nm wide, approximately 1 micrometer deep nano-pockets, with Nb metal electrodes to result in the formation of a vertical single-pole-double-throw switch architecture.

Structure and regulatory role of the C-terminal winged helix domain of the archaeal minichromosome maintenance complex

PubMed Central

Wiedemann, Christoph; Szambowska, Anna; Häfner, Sabine; Ohlenschläger, Oliver; Gührs, Karl-Heinz; Görlach, Matthias

2015-01-01

The minichromosome maintenance complex (MCM) represents the replicative DNA helicase both in eukaryotes and archaea. Here, we describe the solution structure of the C-terminal domains of the archaeal MCMs of Sulfolobus solfataricus (Sso) and Methanothermobacter thermautotrophicus (Mth). Those domains consist of a structurally conserved truncated winged helix (WH) domain lacking the two typical ‘wings’ of canonical WH domains. A less conserved N-terminal extension links this WH module to the MCM AAA+ domain forming the ATPase center. In the Sso MCM this linker contains a short α-helical element. Using Sso MCM mutants, including chimeric constructs containing Mth C-terminal domain elements, we show that the ATPase and helicase activity of the Sso MCM is significantly modulated by the short α-helical linker element and by N-terminal residues of the first α-helix of the truncated WH module. Finally, based on our structural and functional data, we present a docking-derived model of the Sso MCM, which implies an allosteric control of the ATPase center by the C-terminal domain. PMID:25712103

α-Helical Structural Elements within the Voltage-Sensing Domains of a K+ Channel

PubMed Central

Li-Smerin, Yingying; Hackos, David H.; Swartz, Kenton J.

2000-01-01

Voltage-gated K+ channels are tetramers with each subunit containing six (S1–S6) putative membrane spanning segments. The fifth through sixth transmembrane segments (S5–S6) from each of four subunits assemble to form a central pore domain. A growing body of evidence suggests that the first four segments (S1–S4) comprise a domain-like voltage-sensing structure. While the topology of this region is reasonably well defined, the secondary and tertiary structures of these transmembrane segments are not. To explore the secondary structure of the voltage-sensing domains, we used alanine-scanning mutagenesis through the region encompassing the first four transmembrane segments in the drk1 voltage-gated K+ channel. We examined the mutation-induced perturbation in gating free energy for periodicity characteristic of α-helices. Our results are consistent with at least portions of S1, S2, S3, and S4 adopting α-helical secondary structure. In addition, both the S1–S2 and S3–S4 linkers exhibited substantial helical character. The distribution of gating perturbations for S1 and S2 suggest that these two helices interact primarily with two environments. In contrast, the distribution of perturbations for S3 and S4 were more complex, suggesting that the latter two helices make more extensive protein contacts, possibly interfacing directly with the shell of the pore domain. PMID:10613917

Structural features of influenza A virus panhandle RNA enabling the activation of RIG-I independently of 5′-triphosphate

PubMed Central

Lee, Mi-Kyung; Kim, Hee-Eun; Park, Eun-Byeol; Lee, Janghyun; Kim, Ki-Hun; Lim, Kyungeun; Yum, Seoyun; Lee, Young-Hoon; Kang, Suk-Jo; Lee, Joon-Hwa; Choi, Byong-Seok

2016-01-01

Retinoic acid-inducible gene I (RIG-I) recognizes specific molecular patterns of viral RNAs for inducing type I interferon. The C-terminal domain (CTD) of RIG-I binds to double-stranded RNA (dsRNA) with the 5′-triphosphate (5′-PPP), which induces a conformational change in RIG-I to an active form. It has been suggested that RIG-I detects infection of influenza A virus by recognizing the 5′-triphosphorylated panhandle structure of the viral RNA genome. Influenza panhandle RNA has a unique structure with a sharp helical bending. In spite of extensive studies of how viral RNAs activate RIG-I, whether the structural elements of the influenza panhandle RNA confer the ability to activate RIG-I signaling has been poorly explored. Here, we investigated the dynamics of the influenza panhandle RNA in complex with RIG-I CTD using NMR spectroscopy and showed that the bending structure of the panhandle RNA negates the requirement of a 5′-PPP moiety for RIG-I activation. PMID:27288441

An asymmetric mesoscopic model for single bulges in RNA

NASA Astrophysics Data System (ADS)

de Oliveira Martins, Erik; Weber, Gerald

2017-10-01

Simple one-dimensional DNA or RNA mesoscopic models are of interest for their computational efficiency while retaining the key elements of the molecular interactions. However, they only deal with perfectly formed DNA or RNA double helices and consider the intra-strand interactions to be the same on both strands. This makes it difficult to describe highly asymmetric structures such as bulges and loops and, for instance, prevents the application of mesoscopic models to determine RNA secondary structures. Here we derived the conditions for the Peyrard-Bishop mesoscopic model to overcome these limitations and applied it to the calculation of single bulges, the smallest and simplest of these asymmetric structures. We found that these theoretical conditions can indeed be applied to any situation where stacking asymmetry needs to be considered. The full set of parameters for group I RNA bulges was determined from experimental melting temperatures using an optimization procedure, and we also calculated average opening profiles for several RNA sequences. We found that guanosine bulges show the strongest perturbation on their neighboring base pairs, considerably reducing the on-site interactions of their neighboring base pairs.

Optimization of micromachined membrane switches

NASA Astrophysics Data System (ADS)

Hiltmann, Kai; Lang, Walter

1997-09-01

We have determined the minimum dimensions for micromachined membrane switches in several experiments, both regarding the strength of the membranes themselves and the elongations required for safe switching performance. Based on these data, pressure switches for voltages of 10 - 100 V were made as single and multiple elements and tested. Test results, with scatter of pressure threshold data in the ten per cent range, prove very encouraging for further development.

Passive electrically switchable circuit element having improved tunability and method for its manufacture

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

Mickel, Patrick R; James, Conrad D

2014-09-16

A resistive switching device and methods for making the same are disclosed. In the above said device, a resistive switching layer is interposed between opposing electrodes. The resistive switching layer comprises at least two sub-layers of switchable insulative material characterized by different ionic mobilities.

Non-solenoidal Startup via Local Helicity Injection on Pegasus: Progress and Plans

NASA Astrophysics Data System (ADS)

Reusch, J. A.; Barr, J. L.; Bodner, G. M.; Bongard, M. W.; Burke, M. G.; Fonck, R. J.; Hinson, E. T.; Lewicki, B. T.; Perry, J. M.; Schlossberg, D. J.

2015-11-01

Non-solenoidal plasma startup via local helicity injection (LHI) at the Pegasus toroidal experiment now provides routine operation at Ip ~ 0.17MA with Iinj ~ 5kA and Vinj ~ 1kV from four active arc injectors. Experiments in the past year have advanced the understanding of the governing physics of LHI and its supporting technology. Injector impedance scales as Vinj3/ 2 and is governed by two effects: a quasineutrality constraint on electron beam propagation, related to the tokamak edge density, and double-layer sheath expansion, related to narc. Injector design improvements permit operation at Vinj >= 1 kV without deleterious PMI or impurity generation. Discharges with varied shape, Ip(t), and helicity input test a predictive 0D power-balance model for LHI startup. Anomalous, reconnection-driven Ti >800 eV and strong MHD activity localized near the injectors are observed during LHI. Preliminary core Thomson scattering measurements indicate surprisingly high Te >300 eV, which if verified may indicate the dominance of high-energy electron fueling from the injector current streams. A new divertor injector system has been designed to substantially increase the available helicity input rate and support critical studies of confinement during LHI and reconnection activity at high Ip. A proposed upgrade to the Pegasus experiment will extend these studies to NSTX-U relevant parameters. Support: US DOE grants DE-FG02-96ER54375; and DE-SC0006928.

Computerized Design and Generation of Low-Noise Gears with Localized Bearing Contact

NASA Technical Reports Server (NTRS)

Litvin, Faydor L.; Chen, Ningxin; Chen, Jui-Sheng; Lu, Jian; Handschuh, Robert F.

1995-01-01

The results of research projects directed at the reduction of noise caused by misalignment of the following gear drives: double-circular arc helical gears, modified involute helical gears, face-milled spiral bevel gears, and face-milled formate cut hypoid gears are presented. Misalignment in these types of gear drives causes periodic, almost linear discontinuous functions of transmission errors. The period of such functions is the cycle of meshing when one pair of teeth is changed for the next. Due to the discontinuity of such functions of transmission errors high vibration and noise are inevitable. A predesigned parabolic function of transmission errors that is able to absorb linear discontinuous functions of transmission errors and change the resulting function of transmission errors into a continuous one is proposed. The proposed idea was successfully tested using spiral bevel gears and the noise was reduced a substantial amount in comparison with the existing design. The idea of a predesigned parabolic function is applied for the reduction of noise of helical and hypoid gears. The effectiveness of the proposed approach has been investigated by developed TCA (tooth contact analysis) programs. The bearing contact for the mentioned gears is localized. Conditions that avoid edge contact for the gear drives have been determined. Manufacturing of helical gears with new topology by hobs and grinding worms has been investigated.

Metal-Free Multiple Carbon-Carbon and Carbon-Hydrogen Bond Activations via Charge-Switching Mechanism in Unstrained Diindolylmethanes.

PubMed

Challa, Chandrasekhar; Varughese, Sunil; Suresh, Cherumuttathu H; Lankalapalli, Ravi S

2017-08-18

A transformation of the unstrained phenol substituted 3,3'-diindolylmethanes (DIPMs) to 2,3'-diindolylketones (DIKs) by double C-C single bond cleavage with associated rearrangements, triggered by phenyliodine(III) diacetate (PIDA), is reported. Density functional theory studies reveal a mechanism involving multiple "charge-switching" steps by synergistic involvement of the two indole units with overall low activation energy. The indole 'charge-switching' mechanism in DIPMs was further extended toward synthesis of a natural product motif cyclohepta[b]indole from biaryl appended DIBM.

One-Joule-per-Pulse Q-Switched 2-micron Solid State Laser

NASA Technical Reports Server (NTRS)

Yu, Jirong; Trieu, Bo C.; Modlin, Ed A.; Singh, Upendra N.; Kavaya, Michael J.; Chen, Songsheng; Bai, Yingxin; Petzar, Pual J.; Petros, Mulugeta

2005-01-01

Q-switched output of 1.1 J per pulse at 2-micron wavelength has been achieved in a diode pumped Ho:Tm:LuLF laser using a side-pumped rod configuration in a Master-Oscillator-Power-Amplifier (MOPA) architecture. This is the first time that a 2-micron laser has broken the Joule per pulse barrier for Q-switched operation. The total system efficiency reaches 5% and 6.2% for single and double pulse operation, respectively. The system produces excellent 1.4 times of transform limited beam quality.

Cryo-EM reconstruction of AlfA from Bacillus subtilis reveals the structure of a simplified actin-like filament at 3.4-Å resolution.

PubMed

Szewczak-Harris, Andrzej; Löwe, Jan

2018-03-27

Low copy-number plasmid pLS32 of Bacillus subtilis subsp. natto contains a partitioning system that ensures segregation of plasmid copies during cell division. The partitioning locus comprises actin-like protein AlfA, adaptor protein AlfB, and the centromeric sequence parN Similar to the ParMRC partitioning system from Escherichia coli plasmid R1, AlfA filaments form actin-like double helical filaments that arrange into an antiparallel bipolar spindle, which attaches its growing ends to sister plasmids through interactions with AlfB and parN Because, compared with ParM and other actin-like proteins, AlfA is highly diverged in sequence, we determined the atomic structure of nonbundling AlfA filaments to 3.4-Å resolution by cryo-EM. The structure reveals how the deletion of subdomain IIB of the canonical actin fold has been accommodated by unique longitudinal and lateral contacts, while still enabling formation of left-handed, double helical, polar and staggered filaments that are architecturally similar to ParM. Through cryo-EM reconstruction of bundling AlfA filaments, we obtained a pseudoatomic model of AlfA doublets: the assembly of two filaments. The filaments are antiparallel, as required by the segregation mechanism, and exactly antiphasic with near eightfold helical symmetry, to enable efficient doublet formation. The structure of AlfA filaments and doublets shows, in atomic detail, how deletion of an entire domain of the actin fold is compensated by changes to all interfaces so that the required properties of polymerization, nucleotide hydrolysis, and antiparallel doublet formation are retained to fulfill the system's biological raison d'être.

Nonvolatile random access memory

NASA Technical Reports Server (NTRS)

Wu, Jiin-Chuan (Inventor); Stadler, Henry L. (Inventor); Katti, Romney R. (Inventor)

1994-01-01

A nonvolatile magnetic random access memory can be achieved by an array of magnet-Hall effect (M-H) elements. The storage function is realized with a rectangular thin-film ferromagnetic material having an in-plane, uniaxial anisotropy and inplane bipolar remanent magnetization states. The thin-film magnetic element is magnetized by a local applied field, whose direction is used to form either a 0 or 1 state. The element remains in the 0 or 1 state until a switching field is applied to change its state. The stored information is detcted by a Hall-effect sensor which senses the fringing field from the magnetic storage element. The circuit design for addressing each cell includes transistor switches for providing a current of selected polarity to store a binary digit through a separate conductor overlying the magnetic element of the cell. To read out a stored binary digit, transistor switches are employed to provide a current through a row of Hall-effect sensors connected in series and enabling a differential voltage amplifier connected to all Hall-effect sensors of a column in series. To avoid read-out voltage errors due to shunt currents through resistive loads of the Hall-effect sensors of other cells in the same column, at least one transistor switch is provided between every pair of adjacent cells in every row which are not turned on except in the row of the selected cell.

Decentralized stabilization of semi-active vibrating structures

NASA Astrophysics Data System (ADS)

Pisarski, Dominik

2018-02-01

A novel method of decentralized structural vibration control is presented. The control is assumed to be realized by a semi-active device. The objective is to stabilize a vibrating system with the optimal rates of decrease of the energy. The controller relies on an easily implemented decentralized switched state-feedback control law. It uses a set of communication channels to exchange the state information between the neighboring subcontrollers. The performance of the designed method is validated by means of numerical experiments performed for a double cantilever system equipped with a set of elastomers with controlled viscoelastic properties. In terms of the assumed objectives, the proposed control strategy significantly outperforms the passive damping cases and is competitive with a standard centralized control. The presented methodology can be applied to a class of bilinear control systems concerned with smart structural elements.

Mathematical modeling of atopic dermatitis reveals "double-switch" mechanisms underlying 4 common disease phenotypes.

PubMed

Domínguez-Hüttinger, Elisa; Christodoulides, Panayiotis; Miyauchi, Kosuke; Irvine, Alan D; Okada-Hatakeyama, Mariko; Kubo, Masato; Tanaka, Reiko J

2017-06-01

The skin barrier acts as the first line of defense against constant exposure to biological, microbial, physical, and chemical environmental stressors. Dynamic interplay between defects in the skin barrier, dysfunctional immune responses, and environmental stressors are major factors in the development of atopic dermatitis (AD). A systems biology modeling approach can yield significant insights into these complex and dynamic processes through integration of prior biological data. We sought to develop a multiscale mathematical model of AD pathogenesis that describes the dynamic interplay between the skin barrier, environmental stress, and immune dysregulation and use it to achieve a coherent mechanistic understanding of the onset, progression, and prevention of AD. We mathematically investigated synergistic effects of known genetic and environmental risk factors on the dynamic onset and progression of the AD phenotype, from a mostly asymptomatic mild phenotype to a severe treatment-resistant form. Our model analysis identified a "double switch," with 2 concatenated bistable switches, as a key network motif that dictates AD pathogenesis: the first switch is responsible for the reversible onset of inflammation, and the second switch is triggered by long-lasting or frequent activation of the first switch, causing irreversible onset of systemic T H 2 sensitization and worsening of AD symptoms. Our mathematical analysis of the bistable switch predicts that genetic risk factors decrease the threshold of environmental stressors to trigger systemic T H 2 sensitization. This analysis predicts and explains 4 common clinical AD phenotypes from a mild and reversible phenotype through to severe and recalcitrant disease and provides a mechanistic explanation for clinically demonstrated preventive effects of emollient treatments against development of AD. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Scalable Active Optical Access Network Using Variable High-Speed PLZT Optical Switch/Splitter

NASA Astrophysics Data System (ADS)

Ashizawa, Kunitaka; Sato, Takehiro; Tokuhashi, Kazumasa; Ishii, Daisuke; Okamoto, Satoru; Yamanaka, Naoaki; Oki, Eiji

This paper proposes a scalable active optical access network using high-speed Plumbum Lanthanum Zirconate Titanate (PLZT) optical switch/splitter. The Active Optical Network, called ActiON, using PLZT switching technology has been presented to increase the number of subscribers and the maximum transmission distance, compared to the Passive Optical Network (PON). ActiON supports the multicast slot allocation realized by running the PLZT switch elements in the splitter mode, which forces the switch to behave as an optical splitter. However, the previous ActiON creates a tradeoff between the network scalability and the power loss experienced by the optical signal to each user. It does not use the optical power efficiently because the optical power is simply divided into 0.5 to 0.5 without considering transmission distance from OLT to each ONU. The proposed network adopts PLZT switch elements in the variable splitter mode, which controls the split ratio of the optical power considering the transmission distance from OLT to each ONU, in addition to PLZT switch elements in existing two modes, the switching mode and the splitter mode. The proposed network introduces the flexible multicast slot allocation according to the transmission distance from OLT to each user and the number of required users using three modes, while keeping the advantages of ActiON, which are to support scalable and secure access services. Numerical results show that the proposed network dramatically reduces the required number of slots and supports high bandwidth efficiency services and extends the coverage of access network, compared to the previous ActiON, and the required computation time for selecting multicast users is less than 30msec, which is acceptable for on-demand broadcast services.

Information analysis of sequences that bind the replication initiator RepA | Center for Cancer Research

Cancer.gov

The tall letters represent the highly conserved bases in DNA binding sites of several prokaryotic repressors and activators. Conservation is strongest where major grooves of the double helical DNA (represented by crests of a cosine wave) face the protein. This shows that conservation analysis alone can be used to predict the face of DNA that contacts the proteins.

Trio of Tryptophans Aid in Camptothecin Therapy | Center for Cancer Research

Cancer.gov

On occasion, a normally desirable feature becomes not so desirable, making it necessary to find ways to work around it. The double helical nature of DNA helps it attain a compact, supercoiled state, which is essential for lengthy strands of DNA to reside in the nucleus as part of the chromosomes. During DNA replication and gene transcription, however, cellular machinery needs

Spontaneous translocation of antitumor oxaliplatin, its enantiomeric analogue, and Cisplatin from one strand to another in double-helical DNA.

PubMed

Malina, Jaroslav; Natile, Giovanni; Brabec, Viktor

2013-09-02

Oxaliplatin and cisplatin belong to the class of platinum-based anticancer agents. Formation of DNA adducts by these complexes and the consequences for its structure and function, is the mechanistic paradigm by which these drugs exert their antitumor activity. We show that employing short oligonucleotide duplexes containing single, site-specific 1,3-intrastrand cross-links of oxaliplatin, its enantiomeric analogue, or cisplatin and by using gel electrophoresis that under physiological conditions the coordination bonds between platinum and the N7 position of guanine residues involved in the cross-links of the Pt(II) complexes can be cleaved. This cleavage may lead to linkage isomerization reactions between these metallodrugs and double-helical DNA. For instance, approximately 25 % 1,3-intrastrand cross-links of the platinum complexes isomerized after 192 h (at 310 K in 200 mM NaClO4). Differential scanning calorimetry of duplexes containing single, site-specific cross-links of oxaliplatin, its enantiomeric analogue, and cisplatin reveals that one of the driving forces that leads to the lability of DNA cross-links of these metallodrugs is a difference between the thermodynamic destabilization induced by the cross-link and by the adduct into which it could isomerize. The rearrangements may proceed in the way that cross-links originally formed in one strand of the DNA can spontaneously translocate from one DNA strand to its complementary counterpart, which may evoke walking of the platinum complex on DNA molecule. In addition, the differences in the kinetics of the rearrangement reactions and the thermodynamic destabilization of DNA observed for adducts of oxaliplatin and its enantiomeric analogue confirm that the chirality at the carrier 1,2-diaminocyclohexane ligand can considerably affect structural and other physical properties of DNA adducts and consequently their biological effects. In aggregate, interesting generalization of the results described in this work might be that the migration of oxaliplatin, its enantiomeric analogue, or cisplatin from one strand to another in double-helical DNA controlled by energetic signatures of these agents might contribute to a better understanding of their cytotoxic and mutagenic potential. Copyright © 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim.

Shuttle-promoted nano-mechanical current switch

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

Song, Taegeun, E-mail: tsong@ictp.it; Kiselev, Mikhail N.; Gorelik, Leonid Y.

2015-09-21

We investigate electron shuttling in three-terminal nanoelectromechanical device built on a movable metallic rod oscillating between two drains. The device shows a double-well shaped electromechanical potential tunable by a source-drain bias voltage. Four stationary regimes controllable by the bias are found for this device: (i) single stable fixed point, (ii) two stable fixed points, (iii) two limit cycles, and (iv) single limit cycle. In the presence of perpendicular magnetic field, the Lorentz force makes possible switching from one electromechanical state to another. The mechanism of tunable transitions between various stable regimes based on the interplay between voltage controlled electromechanical instabilitymore » and magnetically controlled switching is suggested. The switching phenomenon is implemented for achieving both a reliable active current switch and sensoring of small variations of magnetic field.« less

The DEAD-Box Protein CYT-19 Uses Arginine Residues in Its C-Tail To Tether RNA Substrates.

PubMed

Busa, Veronica F; Rector, Maxwell J; Russell, Rick

2017-07-18

DEAD-box proteins are nonprocessive RNA helicases that play diverse roles in cellular processes. The Neurospora crassa DEAD-box protein CYT-19 promotes mitochondrial group I intron splicing and functions as a general RNA chaperone. CYT-19 includes a disordered, arginine-rich "C-tail" that binds RNA, positioning the helicase core to capture and unwind nearby RNA helices. Here we probed the C-tail further by varying the number and positions of arginines within it. We found that removing sets of as few as four of the 11 arginines reduced RNA unwinding activity (k cat /K M ) to a degree equivalent to that seen upon removal of the C-tail, suggesting that a minimum or "threshold" number of arginines is required. In addition, a mutant with 16 arginines displayed RNA unwinding activity greater than that of wild-type CYT-19. The C-tail modifications impacted unwinding only of RNA helices within constructs that included an adjacent helix or structured RNA element that would allow C-tail binding, indicating that the helicase core remained active in the mutants. In addition, changes in RNA unwinding efficiency of the mutants were mirrored by changes in functional RNA affinity, as determined from the RNA concentration dependence of ATPase activity, suggesting that the C-tail functions primarily to increase RNA affinity. Interestingly, the salt concentration dependence of RNA unwinding activity is unaffected by C-tail composition, suggesting that the C-tail uses primarily hydrogen bonding, not electrostatic interactions, to bind double-stranded RNA. Our results provide insights into how an unstructured C-tail contributes to DEAD-box protein activity and suggest parallels with other families of RNA- and DNA-binding proteins.

Multilayer Patch Antenna Surrounded by a Metallic Wall

NASA Technical Reports Server (NTRS)

Zawadzki, Mark; Huang, John

2003-01-01

A multilayer patch antenna, similar to a Yagi antenna, surrounded by a metallic wall has been devised to satisfy requirements to fit within a specified size and shape and to generate a beam with a half-power angular width of <=40 deg. This antenna provides a gain of about 14 dB; in contrast, the gain of a typical single-patch antenna lies between 5 and 6 dB. This antenna can be considered an alternative to a two-dimensional array of patch antenna elements, or to a horn or helical antenna. Unlike a two-dimensional array of patches, this antenna can function without need for a power-division network (unless circular polarization is needed). The profile of this antenna is lower than that of a horn or a helical antenna designed for the same frequency. The primary disadvantage of this antenna, relative to a horn or a helical antenna, is that its footprint is slightly larger.

Propulsion by a helical flagellum in a capillary tube

NASA Astrophysics Data System (ADS)

Liu, Bin; Breuer, Kenneth S.; Powers, Thomas R.

2014-01-01

We study the microscale propulsion of a rotating helical filament confined by a cylindrical tube, using a boundary-element method for Stokes flow that accounts for helical symmetry. We determine the effect of confinement on swimming speed and power consumption. Except for a small range of tube radii at the tightest confinements, the swimming speed at fixed rotation rate increases monotonically as the confinement becomes tighter. At fixed torque, the swimming speed and power consumption depend only on the geometry of the filament centerline, except at the smallest pitch angles for which the filament thickness plays a role. We find that the "normal" geometry of Escherichia coli flagella is optimized for swimming efficiency, independent of the degree of confinement. The efficiency peaks when the arc length of the helix within a pitch matches the circumference of the cylindrical wall. We also show that a swimming helix in a tube induces a net flow of fluid along the tube.

Method of pedestal and common-mode noise correction for switched-capacitor analog memories

DOEpatents

Britton, Charles L.

1996-01-01

A method and apparatus for correcting common-mode noise and pedestal noise in a multichannel array of switched-capacitor analog memories wherein each analog memory is connected to an associated analog-to-digital converter. The apparatus comprises a single differential element in two different embodiments. In a first embodiment, the differential element is a reference analog memory connected to a buffer. In the second embodiment, the differential element is a reference analog memory connected to a reference analog-to-digital connected to an array of digital summing circuits.