SU-E-T-197: Helical Cranial-Spinal Treatments with a Linear Accelerator

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

Anderson, J; Bernard, D; Liao, Y

2014-06-01

Purpose: Craniospinal irradiation (CSI) of systemic disease requires a high level of beam intensity modulation to reduce dose to bone marrow and other critical structures. Current helical delivery machines can take 30 minutes or more of beam-on time to complete these treatments. This pilot study aims to test the feasibility of performing helical treatments with a conventional linear accelerator using longitudinal couch travel during multiple gantry revolutions. Methods: The VMAT optimization package of the Eclipse 10.0 treatment planning system was used to optimize pseudo-helical CSI plans of 5 clinical patient scans. Each gantry revolution was divided into three 120° arcsmore » with each isocenter shifted longitudinally. Treatments requiring more than the maximum 10 arcs used multiple plans with each plan after the first being optimized including the dose of the others (Figure 1). The beam pitch was varied between 0.2 and 0.9 (couch speed 5- 20cm/revolution and field width of 22cm) and dose-volume histograms of critical organs were compared to tomotherapy plans. Results: Viable pseudo-helical plans were achieved using Eclipse. Decreasing the pitch from 0.9 to 0.2 lowered the maximum lens dose by 40%, the mean bone marrow dose by 2.1% and the maximum esophagus dose by 17.5%. (Figure 2). Linac-based helical plans showed dose results comparable to tomotherapy delivery for both target coverage and critical organ sparing, with the D50 of bone marrow and esophagus respectively 12% and 31% lower in the helical linear accelerator plan (Figure 3). Total mean beam-on time for the linear accelerator plan was 8.3 minutes, 54% faster than the tomotherapy average for the same plans. Conclusions: This pilot study has demonstrated the feasibility of planning pseudo-helical treatments for CSI targets using a conventional linac and dynamic couch movement, and supports the ongoing development of true helical optimization and delivery.« less

Evolution of hydromagnetic turbulence from the electroweak phase transition

NASA Astrophysics Data System (ADS)

Brandenburg, Axel; Kahniashvili, Tina; Mandal, Sayan; Pol, Alberto Roper; Tevzadze, Alexander G.; Vachaspati, Tanmay

2017-12-01

We present new simulations of decaying hydromagnetic turbulence for a relativistic equation of state relevant to the early Universe. We compare helical and nonhelical cases either with kinetically or magnetically dominated initial fields. Both kinetic and magnetic initial helicities lead to maximally helical magnetic fields after some time, but with different temporal decay laws. Both are relevant to the early Universe, although no mechanisms have yet been identified that produce magnetic helicity with strengths comparable to the big bang nucleosynthesis limit at scales comparable to the Hubble horizon at the electroweak phase transition. Nonhelical magnetically dominated fields could still produce picoGauss magnetic fields under most optimistic conditions. Only helical magnetic fields can potentially have nanoGauss strengths at scales up to 30 kpc today.

A combined study of photospheric magnetic and current helicities and subsurface kinetic helicities of solar active regions during 2006-2013

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

Seligman, D.; Petrie, G. J. D.; Komm, R.

2014-11-10

We compare the average photospheric current helicity H{sub c} , photospheric twist parameter α (a well-known proxy for the full relative magnetic helicity), and subsurface kinetic helicity H{sub k} for 194 active regions observed between 2006-2013. We use 2440 Hinode photospheric vector magnetograms, and the corresponding subsurface fluid velocity data derived from GONG (2006-2012) and Helioseismic and Magnetic Imager (2010-2013) dopplergrams. We find a significant hemispheric bias in all three parameters. The subsurface kinetic helicity is preferentially positive in the southern hemisphere and negative in the northern hemisphere. The photospheric current helicity and the α parameter have the same biasmore » for strong fields (|B| > 1000 G) and no significant bias for weak fields (100 G <|B| < 500 G). We find no significant region-by-region correlation between the subsurface kinetic helicity and either the strong-field current helicity or α. Subsurface fluid motions of a given handedness correspond to photospheric helicities of both signs in approximately equal numbers. However, common variations appear in annual averages of these quantities over all regions. Furthermore, in a subset of 77 regions, we find significant correlations between the temporal profiles of the subsurface and photospheric helicities. In these cases, the sign of the linear correlation coefficient matches the sign relationship between the helicities, indicating that the photospheric magnetic field twist is sensitive to the twisting motions below the surface.« less

Radiographic Review of Helical Blade Versus Lag Screw Fixation for Cephalomedullary Nailing of Low-Energy Peritrochanteric Femur Fractures: There is a Difference in Cutout.

PubMed

Stern, Lorraine C; Gorczyca, John T; Kates, Stephen; Ketz, John; Soles, Gillian; Humphrey, Catherine A

2017-06-01

To compare the rate of cutout of helical blades and lag screws in low-energy peritrochanteric femur fractures treated with a cephalomedullary nail (CMN). Retrospective review. Academic medical center. Overall, this study included 362 patients with an average age of 83 year old, a majority of whom were women, and had sustained a low-energy peritrochanteric femur fracture treated with a CMN. All patients had at least 3 months of clinical and radiographic follow, with an average follow-up of 11 months and a range of 3-88 months follow-up. Cephalomedullary nailing with the use of a helical blade or single lag screw for proximal fixation. Cutout of the helical blade or lag screw. Twenty-two cutouts occurred, 14 (15.1%) of 93 patients with helical blades and 8 (3.0%) of 269 patients with lag screws. Cutout with the helical blade was significantly more frequent than with the lag screw (P = 0.0001). The average tip-apex distance (TAD) was significantly greater for those patients who experienced cutout both for the helical blades (23.5 vs. 19.7 mm; P = 0.0194) and lag screws (24.5 vs. 20.0 mm; P = 0.0197). An absolute TAD predictive of cutout could not be determined. When the helical blade was used, implant cutout occurred at a significantly higher rate compared with lag screw fixation. There was not a threshold TAD that was predictive of cutout for either implant. Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.

Helical tomotherapy significantly reduces dose to normal tissues when compared to 3D-CRT for locally advanced rectal cancer.

PubMed

Jhaveri, Pavan M; Teh, Bin S; Paulino, Arnold C; Smiedala, Mindy J; Fahy, Bridget; Grant, Walter; McGary, John; Butler, E Brian

2009-10-01

Combined modality treatment (neoadjuvant chemoradiotherapy followed by surgery) for locally advanced rectal cancer requires special attention to various organs at risk (OAR). As a result, the use of conformal dose delivery methods has become more common in this disease setting. Helical tomotherapy is an image-guided intensity modulated delivery system that delivers dose in a fan-beam manner at 7 degree intervals around the patient and can potentially limit normal tissue from high dose radiation while adequately treating targets. In this study we dosimetrically compare helical tomotherapy to 3D-CRT for stage T3 rectal cancer. The helical tomotherapy plans were optimized in the TomoPlan system to achieve an equivalent uniform dose of 45 Gy for 10 patients with T3N0M0 disease that was at least 5cm from the anal verge. The GTV included the rectal thickening and mass evident on colonoscopy and CT scan as well as with the help of a colorectal surgeon. The CTV included the internal iliac, obturator, and pre-sacral lymphatic chains. The OAR that were outlined included the small bowel, pelvic bone marrow, femoral heads, and bladder. Anatom-e system was used to assist in delineating GTV, CTV and OAR. These 10 plans were then duplicated and optimized into 3-field 3D-CRT plans within the Pinnacle planning system.The V[45], V[40], V[30], V[20], V[10], and mean dose to the OAR were compared between the helical tomotherapy and 3D-CRT plans. Statistically significant differences were achieved in the doses to all OAR, including all volumes and means except for V[10] for the small bowel and the femoral heads. Adequate dosimetric coverage of targets were achieved with both helical tomotherapy and 3D-CRT. Helical tomotherapy reduces the volume of normal tissue receiving high-dose RT when compared to 3D-CRT treatment. Both modalities adequately dose the tumor. Clinical studies addressing the dosimetric benefits are on-going.

Comparison of Image Quality and Radiation Dose of Coronary Computed Tomography Angiography Between Conventional Helical Scanning and a Strategy Incorporating Sequential Scanning

PubMed Central

Einstein, Andrew J.; Wolff, Steven D.; Manheimer, Eric D.; Thompson, James; Terry, Sylvia; Uretsky, Seth; Pilip, Adalbert; Peters, M. Robert

2009-01-01

Radiation dose from coronary computed tomography angiography may be reduced using a sequential scanning protocol rather than a conventional helical scanning protocol. Here we compare radiation dose and image quality from coronary computed tomography angiography in a single center between an initial period during which helical scanning with electrocardiographically-controlled tube current modulation was used for all patients (n=138) and after adoption of a strategy incorporating sequential scanning whenever appropriate (n=261). Using the sequential-if-appropriate strategy, sequential scanning was employed in 86.2% of patients. Compared to the helical-only strategy, this strategy was associated with a 65.1% dose reduction (mean dose-length product of 305.2 vs. 875.1 and mean effective dose of 14.9 mSv vs. 5.2 mSv, respectively), with no significant change in overall image quality, step artifacts, motion artifacts, or perceived image noise. For the 225 patients undergoing sequential scanning, the dose-length product was 201.9 ± 90.0 mGy·cm, while for patients undergoing helical scanning under either strategy, the dose-length product was 890.9 ± 293.3 mGy·cm (p<0.0001), corresponding to mean effective doses of 3.4 mSv and 15.1 mSv, respectively, a 77.5% reduction. Image quality was significantly greater for the sequential studies, reflecting the poorer image quality in patients undergoing helical scanning in the sequential-if-appropriate strategy. In conclusion, a sequential-if-appropriate diagnostic strategy reduces dose markedly compared to a helical-only strategy, with no significant difference in image quality. PMID:19892048

Two-fluid and finite Larmor radius effects on helicity evolution in a plasma pinch

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

Sauppe, J. P., E-mail: jpsauppe@gmail.com; Department of Physics, University of Wisconsin-Madison, 1150 University Avenue, Madison, Wisconsin 53706; Sovinec, C. R., E-mail: csovinec@wisc.edu

2016-03-15

The evolution of magnetic energy, helicity, and hybrid helicity during nonlinear relaxation of a driven-damped plasma pinch is compared in visco-resistive magnetohydrodynamics and two-fluid models with and without the ion gyroviscous stress tensor. Magnetic energy and helicity are supplied via a boundary electric field which initially balances the resistive dissipation, and the plasma undergoes multiple relaxation events during the nonlinear evolution. The magnetic helicity is well conserved relative to the magnetic energy over each event, which is short compared with the global resistive diffusion time. The magnetic energy decreases by roughly 1.5% of its initial value over a relaxation event,more » while the magnetic helicity changes by at most 0.2% of the initial value. The hybrid helicity is dominated by magnetic helicity in low-β pinch conditions and is also well conserved. Differences of less than 1% between magnetic helicity and hybrid helicity are observed with two-fluid modeling and result from cross helicity evolution. The cross helicity is found to change appreciably due to the first-order finite Larmor radius effects which have not been included in contemporary relaxation theories. The plasma current evolves towards the flat parallel current state predicted by Taylor relaxation theory but does not achieve it. Plasma flow develops significant structure for two-fluid models, and the flow perpendicular to the magnetic field is much more substantial than the flow along it.« less

Helical vortices: linear stability analysis and nonlinear dynamics

NASA Astrophysics Data System (ADS)

Selçuk, C.; Delbende, I.; Rossi, M.

2018-02-01

We numerically investigate, within the context of helical symmetry, the dynamics of a regular array of two or three helical vortices with or without a straight central hub vortex. The Navier-Stokes equations are linearised to study the instabilities of such basic states. For vortices with low pitches, an unstable mode is extracted which corresponds to a displacement mode and growth rates are found to compare well with results valid for an infinite row of point vortices or an infinite alley of vortex rings. For larger pitches, the system is stable with respect to helically symmetric perturbations. In the nonlinear regime, we follow the time-evolution of the above basic states when initially perturbed by the dominant instability mode. For two vortices, sequences of overtaking events, leapfrogging and eventually merging are observed. The transition between such behaviours occurs at a critical ratio involving the core size and the vortex-separation distance. Cases with three helical vortices are also presented.

Observation of enhanced radial transport of energetic ion due to energetic particle mode destabilized by helically-trapped energetic ion in the Large Helical Device

NASA Astrophysics Data System (ADS)

Ogawa, K.; Isobe, M.; Kawase, H.; Nishitani, T.; Seki, R.; Osakabe, M.; LHD Experiment Group

2018-04-01

A deuterium experiment was initiated to achieve higher-temperature and higher-density plasmas in March 2017 in the Large Helical Device (LHD). The central ion temperature notably increases compared with that in hydrogen experiments. However, an energetic particle mode called the helically-trapped energetic-ion-driven resistive interchange (EIC) mode is often excited by intensive perpendicular neutral beam injections on high ion-temperature discharges. The mode leads to significant decrease of the ion temperature or to limiting the sustainment of the high ion-temperature state. To understand the effect of EIC on the energetic ion confinement, the radial transport of energetic ions is studied by means of the neutron flux monitor and vertical neutron camera newly installed on the LHD. Decreases of the line-integrated neutron profile in core channels show that helically-trapped energetic ions are lost from the plasma.

Signatures of unfolding in the early stages of protein denaturation

NASA Astrophysics Data System (ADS)

Gray, Harry B.; Winkler, Jay R.; Kozak, John J.

2012-04-01

A comparative study of the early stages of unfolding of five proteins: cyt c, c-b 562, cyt c‧, azurin, and lysozyme is reported. From crystallographic data, helical regions and intervening non-helical (or 'turning') regions are identified in each. Exploiting a previously introduced geometrical model, the paper describes quantitatively the stepwise extension of a polypeptide chain subject to the geometrical constraint that the spatial relationship among the residues of each triplet is fixed by native-state crystallographic data. Despite differences among the above-cited proteins, remarkable universality of behavior is found in the early stages of unfolding. At the very earliest stages, internal residues in each helical region have a common unfolding history; the terminal residues, however, are extraordinarily sensitive to structural perturbations. Residues in non-helical sections of the polypeptide unfold after residues in the internal helical regions, but with increasing steric perturbation playing a dominant role in advancing denaturation.

DNS of helicity-induced stratified turbulent flow

NASA Astrophysics Data System (ADS)

Chandy, Abhilash J.; Rahimi, Abbas

2013-11-01

Helical flows undergoing density stratification have wide applications in meteorological phenomena such as dust devils, tornadoes, and hurricanes due to the complexity and disasters caused by them. Direct numerical simulations (DNS) of transition to turbulence in a stably stratified Boussinesq fluid are presented for different rotation and stratification intensities. In order to understand the effect of velocity on the energy cascade, comparisons are made between helicity initiated and non-helical flows. Results show that stratification decelerates the helicity decay and causes velocity and vorticity to align with each other. With respect to the helical and non-helical flow comparisons, the total energy in the presence of stratification decays faster with helicity. In addition, the behavior of length scales were examined by comparing temporal variations of the vertical shearing of velocities. Results showed a growing asymmetry with time in the case of helical flow, while non-helical flow stayed close to begin symmetric.

Magnetic helicity generation in the frame of Kazantsev model

NASA Astrophysics Data System (ADS)

Yushkov, Egor V.; Lukin, Alexander S.

2017-11-01

Using a magnetic dynamo model, suggested by Kazantsev (J. Exp. Theor. Phys. 1968, vol. 26, p. 1031), we study the small-scale helicity generation in a turbulent electrically conducting fluid. We obtain the asymptotic dependencies of dynamo growth rate and magnetic correlation functions on magnetic Reynolds numbers. Special attention is devoted to the comparison of a longitudinal correlation function and a function of magnetic helicity for various conditions of asymmetric turbulent flows. We compare the analytical solutions on small scales with numerical results, calculated by an iterative algorithm on non-uniform grids. We show that the exponential growth of current helicity is simultaneous with the magnetic energy for Reynolds numbers larger than some critical value and estimate this value for various types of asymmetry.

A new experiment to investigate the origin of optical activity using a low energy positron beam of controlled helicity. [molecular biology

NASA Technical Reports Server (NTRS)

Gidley, D. W.; Rich, A.; Van House, J. C.; Zitzewitz, P. W.

1981-01-01

Previous experiments undertaken in search of a correlation between the origin of optical activity in biological molecules and the helicity of beta particles emitted in nuclear beta decay have not provided any useful results. A description is presented of an experiment in which a low energy polarized positron beam of controlled helicity interacts with an optically active material to form positronium in vacuum. Advantages of the current study compared to the previous experiments are mainly related to a much greater sensitivity. Initially, it will be possible to detect a helicity-dependent asymmetry in triplet positronium formation of 1 part in 10,000. Improvements to better than 1 part in 100,000 should be attainable.

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.

CURRENT AND KINETIC HELICITY OF LONG-LIVED ACTIVITY COMPLEXES

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

Komm, Rudolf; Gosain, Sanjay, E-mail: komm@nso.edu

2015-01-01

We study long-lived activity complexes and their current helicity at the solar surface and their kinetic helicity below the surface. The current helicity has been determined from synoptic vector magnetograms from the NSO/SOLIS facility, and the kinetic helicity of subsurface flows has been determined with ring-diagram analysis applied to full-disk Dopplergrams from NSO/GONG and SDO/HMI. Current and kinetic helicity of activity complexes follow the hemispheric helicity rule with mainly positive values (78%; 78%, respectively, with a 95% confidence level of 31%) in the southern hemisphere and negative ones (80%; 93%, respectively, with a 95% confidence level of 22% and 14%,more » respectively) in the northern hemisphere. The locations with the dominant sign of kinetic helicity derived from Global Oscillation Network Group (GONG) and SDO/HMI data are more organized than those of the secondary sign even if they are not part of an activity complex, while locations with the secondary sign are more fragmented. This is the case for both hemispheres even for the northern one where it is not as obvious visually due to the large amount of magnetic activity present as compared to the southern hemisphere. The current helicity shows a similar behavior. The dominant sign of current helicity is the same as that of kinetic helicity for the majority of the activity complexes (83% with a 95% confidence level of 15%). During the 24 Carrington rotations analyzed here, there is at least one longitude in each hemisphere where activity complexes occur repeatedly throughout the epoch. These ''active'' longitudes are identifiable as locations of strong current and kinetic helicity of the same sign.« less

Mechanical and structural characteristics of the new BONE-LOK cortical-cancellous internal fixation device.

PubMed

Cachia, Victor V; Culbert, Brad; Warren, Chris; Oka, Richard; Mahar, Andrew

2003-01-01

The purpose of this study was to evaluate the structural and mechanical characteristics of a new and unique titanium cortical-cancellous helical compression anchor with BONE-LOK (Triage Medical, Inc., Irvine, CA) technology for compressive internal fixation of fractures and osteotomies. This device provides fixation through the use of a distal helical anchor and a proximal retentive collar that are united by an axially movable pin (U.S. and international patents issued and pending). The helical compression anchor (2.7-mm diameter) was compared with 3.0-mm diameter titanium cancellous screws (Synthes, Paoli, PA) for pullout strength and compression in 7# and 12# synthetic rigid polyurethane foam (simulated bone matrix), and for 3-point bending stiffness. The following results (mean +/- standard deviation) were obtained: foam block pullout strength in 12# foam: 2.7-mm helical compression anchor 70 +/- 2.0 N and 3.0-mm titanium cancellous screws 37 +/- 11 N; in 7# foam: 2.7-mm helical compression anchor 33 +/- 3 N and 3.0-mm titanium cancellous screws 31 +/- 12 N. Three-point bending stiffness, 2.7-mm helical compression anchor 988 +/- 68 N/mm and 3.0-mm titanium cancellous screws 845 +/- 88 N/mm. Compression strength testing in 12# foam: 2.7-mm helical compression anchor 70.8 +/- 4.8 N and 3.0-mm titanium cancellous screws 23.0 +/- 3.1 N, in 7# foam: 2.7-mm helical compression anchor 42.6 +/- 3.2 N and 3.0-mm titanium cancellous screws 10.4 +/- 0.9 N. Results showed greater pullout strength, 3-point bending stiffness, and compression strength for the 2.7-mm helical compression anchor as compared with the 3.0-mm titanium cancellous screws in these testing models. This difference represents a distinct advantage in the new device that warrants further in vivo testing.

Numerical Analysis of Helical Pile-Soil Interaction under Compressive Loads

NASA Astrophysics Data System (ADS)

Polishchuk, A. I.; Maksimov, F. A.

2017-11-01

The results of the field tests of full-scale steel helical piles in clay soils intended for prefabricated temporary buildings foundations are presented in this article. The finite element modeling was used for the evaluation of stress distribution of the clay soil around helical piles. An approach of modeling of the screw-pile geometry has been proposed through the Finite Element Analysis. Steel helical piles with a length of 2.0 m, shaft diameter of 0.108 m and a blade diameter of 0.3 m were used in the experiments. The experiments have shown the efficiency of double-bladed helical piles in the clay soils compared to single-bladed piles. It has been experimentally established that the introduction of the second blade into the pile shaft provides an increase of the bearing capacity in clay soil up to 30% compared to a single-bladed helical pile with similar geometrical dimensions. The numerical results are compared with the measurements obtained by a large scale test and the bearing capacity has been estimated. It has been found that the model results fit the field results. For a double-bladed helical pile it was revealed that shear stresses upon pile loading are formed along the lateral surface forming a cylindrical failure surface.

Molecular dynamics simulations of membrane deformation induced by amphiphilic helices of Epsin, Sar1p, and Arf1

NASA Astrophysics Data System (ADS)

Li, Zhen-Lu

2018-03-01

The N-terminal amphiphilic helices of proteins Epsin, Sar1p, and Arf1 play a critical role in initiating membrane deformation. The interactions of these amphiphilic helices with the lipid membranes are investigated in this study by combining the all-atom and coarse-grained simulations. In the all-atom simulations, the amphiphilic helices of Epsin and Sar1p are found to have a shallower insertion depth into the membrane than the amphiphilic helix of Arf1, but remarkably, the amphiphilic helices of Epsin and Sar1p induce higher asymmetry in the lipid packing between the two monolayers of the membrane. The insertion depth of amphiphilic helix into the membrane is determined not only by the overall hydrophobicity but also by the specific distributions of polar and non-polar residues along the helix. To directly compare their ability to deform the membrane, the coarse-grained simulations are performed to investigate the membrane deformation under the insertion of multiple helices. Project supported by the National Natural Science Foundation of China (Grant Nos. 91427302 and 11474155).

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.

ON ASYMMETRY OF MAGNETIC HELICITY IN EMERGING ACTIVE REGIONS: HIGH-RESOLUTION OBSERVATIONS

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

Tian Lirong; Alexander, David; Zhu Chunming

We employ the DAVE (differential affine velocity estimator) tracking technique on a time series of Michelson Doppler Imager (MDI)/1 minute high spatial resolution line-of-sight magnetograms to measure the photospheric flow velocity for three newly emerging bipolar active regions (ARs). We separately calculate the magnetic helicity injection rate of the leading and following polarities to confirm or refute the magnetic helicity asymmetry, found by Tian and Alexander using MDI/96 minute low spatial resolution magnetograms. Our results demonstrate that the magnetic helicity asymmetry is robust, being present in the three ARs studied, two of which have an observed balance of the magneticmore » flux. The magnetic helicity injection rate measured is found to depend little on the window size selected, but does depend on the time interval used between the two successive magnetograms being tracked. It is found that the measurement of the magnetic helicity injection rate performs well for a window size between 12 x 10 and 18 x 15 pixels and at a time interval {Delta}t = 10 minutes. Moreover, the short-lived magnetic structures, 10-60 minutes, are found to contribute 30%-50% of the magnetic helicity injection rate. Comparing with the results calculated by MDI/96 minute data, we find that the MDI/96 minute data, in general, can outline the main trend of the magnetic properties, but they significantly underestimate the magnetic flux in strong field regions and are not appropriate for quantitative tracking studies, so provide a poor estimate of the amount of magnetic helicity injected into the corona.« less

Magnetic Helicity Estimations in Models and Observations of the Solar Magnetic Field. III. Twist Number Method

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

Guo, Y.; Pariat, E.; Moraitis, K.

We study the writhe, twist, and magnetic helicity of different magnetic flux ropes, based on models of the solar coronal magnetic field structure. These include an analytical force-free Titov–Démoulin equilibrium solution, non-force-free magnetohydrodynamic simulations, and nonlinear force-free magnetic field models. The geometrical boundary of the magnetic flux rope is determined by the quasi-separatrix layer and the bottom surface, and the axis curve of the flux rope is determined by its overall orientation. The twist is computed by the Berger–Prior formula, which is suitable for arbitrary geometry and both force-free and non-force-free models. The magnetic helicity is estimated by the twistmore » multiplied by the square of the axial magnetic flux. We compare the obtained values with those derived by a finite volume helicity estimation method. We find that the magnetic helicity obtained with the twist method agrees with the helicity carried by the purely current-carrying part of the field within uncertainties for most test cases. It is also found that the current-carrying part of the model field is relatively significant at the very location of the magnetic flux rope. This qualitatively explains the agreement between the magnetic helicity computed by the twist method and the helicity contributed purely by the current-carrying magnetic field.« less

Unenhanced 320-row multidetector computed tomography of the brain in children: comparison of image quality and radiation dose among wide-volume, one-shot volume, and helical scan modes.

PubMed

Jeon, Sun Kyung; Choi, Young Hun; Cheon, Jung-Eun; Kim, Woo Sun; Cho, Yeon Jin; Ha, Ji Young; Lee, Seung Hyun; Hyun, Hyejin; Kim, In-One

2018-04-01

The 320-row multidetector computed tomography (CT) scanner has multiple scan modes, including volumetric modes. To compare the image quality and radiation dose of 320-row CT in three acquisition modes - helical, one-shot volume, and wide-volume scan - at pediatric brain imaging. Fifty-seven children underwent unenhanced brain CT using one of three scan modes (helical scan, n=21; one-shot volume scan, n=17; wide-volume scan, n=19). For qualitative analysis, two reviewers evaluated overall image quality and image noise using a 5-point grading system. For quantitative analysis, signal-to-noise ratio, image noise and posterior fossa artifact index were calculated. To measure the radiation dose, adjusted CT dose index per unit volume (CTDI adj ) and dose length product (DLP) were compared. Qualitatively, the wide-volume scan showed significantly less image noise than the helical scan (P=0.009), and less streak artifact than the one-shot volume scan (P=0.001). The helical mode showed significantly lower signal-to-noise ratio, with a higher image noise level compared with the one-shot volume and wide-volume modes (all P<0.05). The CTDI adj and DLP were significantly lower in the one-shot volume and wide-volume modes compared with those in the helical scan mode (all P<0.05). For pediatric unenhanced brain CT, both the wide-volume and one-shot volume scans reduced radiation dose compared to the helical scan mode, while the wide-volume scan mode showed fewer streak artifacts in the skull vertex and posterior fossa than the one-shot volume scan.

A Combined Study of Photospheric Magnetic and Current Helicities and Subsurface Kinetic Helicities of Solar Active Regions during 2006-2012

NASA Astrophysics Data System (ADS)

Seligman, Darryl; Petrie, G.; Komm, R.

2014-01-01

We compare the average photospheric current helicity H_c, photospheric twist parameter α (a well-known proxy for the full relative magnetic helicity), and subsurface kinetic helicity K_h for 128 active regions observed between 2006-2012. We use 1436 Hinode photospheric vector magnetograms and subsurface fluid velocity data from GONG Dopplergrams. We find a significant hemispheric bias in all three parameters. The K_h parameter is preferentially positive/negative in the southern/northern hemisphere. The H_c and α parameters have the same bias for strong fields |{B}|>1000 G). We examine the temporal variability of each parameter for each active region and identify a significant subset of regions whose three helicity parameters all exhibit clear increasing or decreasing trends. The temporal profiles of these regions have the same bias: positive/negative helicity in the northern/southern hemisphere. The results are consistent with Longcope et al.'s Σ-effect. This work is carried out through the National Solar Observatory Research Experiences for Undergraduate (REU) site program, which is co-funded by the Department of Defense in partnership with the NSF REU Program. The National Solar Observatory is operated by the Association of Universities for Research in Astronomy, Inc. (AURA) under cooperative agreement with the National Science Foundation.

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).

Conversion of Natively Unstructured α-Synuclein to Its α-Helical Conformation Significantly Attenuates Production of Reactive Oxygen Species

PubMed Central

Zhou, Binbin; Hao, Yuanqiang; Wang, Chengshan; Li, Ding; Liu, You-Nian; Zhou, Feimeng

2012-01-01

The intracellular α-synuclein (α-syn) protein, whose conformational change and aggregation have been closely linked to the pathology of Parkingson’s disease (PD), is highly populated at the presynaptic termini and remains there in the α-helical conformation. In this study, circular dichroism confirmed that natively unstructured α-syn in aqueous solution was transformed to its α-helical conformation upon addition of trifluoroethanol (TFE). Electrochemical and UV–visible spectroscopic experiments reveal that both Cu(I) and Cu(II) are stabilized, with the former being stabilized by about two orders of magnitude. Compared to unstructured α-syn (Binolfi et al., J. Am. Chem. Soc. 133 (2011) 194–196), α-helical α-syn stabilizes Cu(I) by more than three orders of magnitude. Through the measurements of H2O2 and hydroxyl radicals (OH•) in solutions containing different forms of Cu(II) (free and complexed by unstructured or α-helical α-syn), we demonstrate that the significantly enhanced Cu(I) binding affinity helps inhibit the production of highly toxic reactive oxygen species, especially the hydroxyl radicals. Our study provides strong evidence that, as a possible means to prevent neuronal cell damage, conversion of the natively unstructured α-syn to its α-helical conformation in vivo could significantly attenuate the copper-modulated ROS production. PMID:23123341

Transmembrane helices containing a charged arginine are thermodynamically stable.

PubMed

Ulmschneider, Martin B; Ulmschneider, Jakob P; Freites, J Alfredo; von Heijne, Gunnar; Tobias, Douglas J; White, Stephen H

2017-10-01

Hydrophobic amino acids are abundant in transmembrane (TM) helices of membrane proteins. Charged residues are sparse, apparently due to the unfavorable energetic cost of partitioning charges into nonpolar phases. Nevertheless, conserved arginine residues within TM helices regulate vital functions, such as ion channel voltage gating and integrin receptor inactivation. The energetic cost of arginine in various positions along hydrophobic helices has been controversial. Potential of mean force (PMF) calculations from atomistic molecular dynamics simulations predict very large energetic penalties, while in vitro experiments with Sec61 translocons indicate much smaller penalties, even for arginine in the center of hydrophobic TM helices. Resolution of this conflict has proved difficult, because the in vitro assay utilizes the complex Sec61 translocon, while the PMF calculations rely on the choice of simulation system and reaction coordinate. Here we present the results of computational and experimental studies that permit direct comparison with the Sec61 translocon results. We find that the Sec61 translocon mediates less efficient membrane insertion of Arg-containing TM helices compared with our computational and experimental bilayer-insertion results. In the simulations, a combination of arginine snorkeling, bilayer deformation, and peptide tilting is sufficient to lower the penalty of Arg insertion to an extent such that a hydrophobic TM helix with a central Arg residue readily inserts into a model membrane. Less favorable insertion by the translocon may be due to the decreased fluidity of the endoplasmic reticulum (ER) membrane compared with pure palmitoyloleoyl-phosphocholine (POPC). Nevertheless, our results provide an explanation for the differences between PMF- and experiment-based penalties for Arg burial.

Non-linearity of the collagen triple helix in solution and implications for collagen function.

PubMed

Walker, Kenneth T; Nan, Ruodan; Wright, David W; Gor, Jayesh; Bishop, Anthony C; Makhatadze, George I; Brodsky, Barbara; Perkins, Stephen J

2017-06-16

Collagen adopts a characteristic supercoiled triple helical conformation which requires a repeating (Xaa-Yaa-Gly) n sequence. Despite the abundance of collagen, a combined experimental and atomistic modelling approach has not so far quantitated the degree of flexibility seen experimentally in the solution structures of collagen triple helices. To address this question, we report an experimental study on the flexibility of varying lengths of collagen triple helical peptides, composed of six, eight, ten and twelve repeats of the most stable Pro-Hyp-Gly (POG) units. In addition, one unblocked peptide, (POG) 10unblocked , was compared with the blocked (POG) 10 as a control for the significance of end effects. Complementary analytical ultracentrifugation and synchrotron small angle X-ray scattering data showed that the conformations of the longer triple helical peptides were not well explained by a linear structure derived from crystallography. To interpret these data, molecular dynamics simulations were used to generate 50 000 physically realistic collagen structures for each of the helices. These structures were fitted against their respective scattering data to reveal the best fitting structures from this large ensemble of possible helix structures. This curve fitting confirmed a small degree of non-linearity to exist in these best fit triple helices, with the degree of bending approximated as 4-17° from linearity. Our results open the way for further studies of other collagen triple helices with different sequences and stabilities in order to clarify the role of molecular rigidity and flexibility in collagen extracellular and immune function and disease. © 2017 The Author(s).

Helical wire stress analysis of unbonded flexible riser under irregular response

NASA Astrophysics Data System (ADS)

Wang, Kunpeng; Ji, Chunyan

2017-06-01

A helical wire is a critical component of an unbonded flexible riser prone to fatigue failure. The helical wire has been the focus of much research work in recent years because of the complex multilayer construction of the flexible riser. The present study establishes an analytical model for the axisymmetric and bending analyses of an unbonded flexible riser. The interlayer contact under axisymmetric loads in this model is modeled by setting radial dummy springs between adjacent layers. The contact pressure is constant during the bending response and applied to determine the slipping friction force per unit helical wire. The model tracks the axial stress around the angular position at each time step to calculate the axial force gradient, then compares the axial force gradient with the slipping friction force to judge the helical wire slipping region, which would be applied to determine the bending stiffness for the next time step. The proposed model is verified against the experimental data in the literature. The bending moment-curvature relationship under irregular response is also qualitatively discussed. The stress at the critical point of the helical wire is investigated based on the model by considering the local flexure. The results indicate that the present model can well simulate the bending stiffness variation during irregular response, which has significant effect on the stress of helical wire.

CFD analysis of the two-phase bubbly flow characteristics in helically coiled rectangular and circular tube heat exchangers

NASA Astrophysics Data System (ADS)

Hussain, Alamin; Fsadni, Andrew M.

2016-03-01

Due to their ease of manufacture, high heat transfer efficiency and compact design, helically coiled heat exchangers are increasingly being adopted in a number of industries. The higher heat transfer efficiency over straight pipes is due to the secondary flow that develops as a result of the centrifugal force. In spite of the widespread use of helically coiled heat exchangers, and the presence of bubbly two-phase flow in a number of systems, very few studies have investigated the resultant flow characteristics. This paper will therefore present the results of CFD simulations for the two-phase bubbly flow in helically coiled heat exchangers as a function of the volumetric void fraction and the tube cross-section design. The CFD results are compared to the scarce flow visualisation experimental results available in the open literature.

Biomechanical comparison of straight DCP and helical plates for fixation of transverse and oblique bone fractures.

PubMed

Aksakal, Bunyamin; Gurger, Murat; Say, Yakup; Yilmaz, Erhan

2014-01-01

Biomechanical comparison of straight DCP and helical plates for fixation of transversal and oblique tibial bone fractures were analyzed and compared to each other by axial compression, bending and torsion tests. An in vitro osteosynthesis of transverse (TF) and oblique bone fracture (OF) fixations have been analysed on fresh sheep tibias by using the DCP and helical compression plates (HP). Statistically significant differences were found for both DCP and helical plate fixations under axial compression, bending and torsional loads. The strength of fixation systems was in favor of DC plating with exception of the TF-HP fixation group under compression loads and torsional moments. The transvers fracture (TF) stability was found to be higher than that found in oblique fracture (OF) fixed by helical plates (HP). However, under torsional testing, compared to conventional plating, the helical plate fixations provided a higher torsional resistance and strength. The maximum stiffness at axial compression loading and maximum torsional strength was achieved in torsional testing for the TF-HP fixations. From in vitro biomechanical analysis, fracture type and plate fixation system groups showed different responses under different loadings. Consequently, current biomechanical analyses may encourage the usage of helical HP fixations in near future during clinical practice for transverse bone fractures.

Dose reduction of up to 89% while maintaining image quality in cardiovascular CT achieved with prospective ECG gating

NASA Astrophysics Data System (ADS)

Londt, John H.; Shreter, Uri; Vass, Melissa; Hsieh, Jiang; Ge, Zhanyu; Adda, Olivier; Dowe, David A.; Sabllayrolles, Jean-Louis

2007-03-01

We present the results of dose and image quality performance evaluation of a novel, prospective ECG-gated Coronary CT Angiography acquisition mode (SnapShot Pulse, LightSpeed VCT-XT scanner, GE Healthcare, Waukesha, WI), and compare it to conventional retrospective ECG gated helical acquisition in clinical and phantom studies. Image quality phantoms were used to measure noise, slice sensitivity profile, in-plane resolution, low contrast detectability and dose, using the two acquisition modes. Clinical image quality and diagnostic confidence were evaluated in a study of 31 patients scanned with the two acquisition modes. Radiation dose reduction in clinical practice was evaluated by tracking 120 consecutive patients scanned with the prospectively gated scan mode. In the phantom measurements, the prospectively gated mode resulted in equivalent or better image quality measures at dose reductions of up to 89% compared to non-ECG modulated conventional helical scans. In the clinical study, image quality was rated excellent by expert radiologist reviewing the cases, with pathology being identical using the two acquisition modes. The average dose to patients in the clinical practice study was 5.6 mSv, representing 50% reduction compared to a similar patient population scanned with the conventional helical mode.

Modeling the Structure of Helical Assemblies with Experimental Constraints in Rosetta.

PubMed

André, Ingemar

2018-01-01

Determining high-resolution structures of proteins with helical symmetry can be challenging due to limitations in experimental data. In such instances, structure-based protein simulations driven by experimental data can provide a valuable approach for building models of helical assemblies. This chapter describes how the Rosetta macromolecular package can be used to model homomeric protein assemblies with helical symmetry in a range of modeling scenarios including energy refinement, symmetrical docking, comparative modeling, and de novo structure prediction. Data-guided structure modeling of helical assemblies with experimental information from electron density, X-ray fiber diffraction, solid-state NMR, and chemical cross-linking mass spectrometry is also described.

Generation of a Large-scale Magnetic Field in a Convective Full-sphere Cross-helicity Dynamo

NASA Astrophysics Data System (ADS)

Pipin, V. V.; Yokoi, N.

2018-05-01

We study the effects of the cross-helicity in the full-sphere large-scale mean-field dynamo models of a 0.3 M ⊙ star rotating with a period of 10 days. In exploring several dynamo scenarios that stem from magnetic field generation by the cross-helicity effect, we found that the cross-helicity provides the natural generation mechanisms for the large-scale scale axisymmetric and nonaxisymmetric magnetic field. Therefore, the rotating stars with convective envelopes can produce a large-scale magnetic field generated solely due to the turbulent cross-helicity effect (we call it γ 2-dynamo). Using mean-field models we compare the properties of the large-scale magnetic field organization that stems from dynamo mechanisms based on the kinetic helicity (associated with the α 2 dynamos) and cross-helicity. For the fully convective stars, both generation mechanisms can maintain large-scale dynamos even for the solid body rotation law inside the star. The nonaxisymmetric magnetic configurations become preferable when the cross-helicity and the α-effect operate independently of each other. This corresponds to situations with purely γ 2 or α 2 dynamos. The combination of these scenarios, i.e., the γ 2 α 2 dynamo, can generate preferably axisymmetric, dipole-like magnetic fields at strengths of several kGs. Thus, we found a new dynamo scenario that is able to generate an axisymmetric magnetic field even in the case of a solid body rotation of the star. We discuss the possible applications of our findings to stellar observations.

High-pitch Helical Dual-source Computed Tomographic Pulmonary Angiography: Comparing Image Quality in Inspiratory Breath-hold and During Free Breathing.

PubMed

Ajlan, Amr M; Binzaqr, Salma; Jadkarim, Dalia A; Jamjoom, Lamia G; Leipsic, Jonathon

2016-01-01

The purpose of this study was to compare qualitative and quantitative image parameters of dual-source high-pitch helical computed tomographic pulmonary angiography (CTPA) in breath-holding (BH) versus free-breathing (FB) patients. Ninety-nine consented patients (61 female individuals; mean age±SD, 49±18.7 y) were randomized into BH (n=45) versus FB (n=54) high-pitch helical CTPA. Patient characteristics and CTPA radiation doses were analyzed. Two readers assessed for pulmonary embolism (PE), transient interruption of contrast, and respiratory and cardiac motion. The readers used a subjective 3-point scale to rate the pulmonary artery opacification and lung parenchymal appearance. A single reader assessed mean pulmonary artery signal intensity, noise, contrast, signal to noise ratio, and contrast to noise ratio. PE was diagnosed in 16% BH and 19% FB patients. CTPAs of both groups were of excellent or acceptable quality for PE evaluation and of similar mean radiation doses (1.3 mSv). Transient interruption of contrast was seen in 5/45 (11%) BH and 5/54 (9%) FB patients (not statistically significant, P=0.54). No statistically significant difference was noted in cardiac, diaphragmatic, and lung parenchymal motion. Lung parenchymal assessment was excellent in all cases, except for 5/54 (9%) motion-affected FB cases with acceptable quality (statistically significant, P=0.03). No CTPA was considered nondiagnostic by any of the readers. No objective image quality differences were noted between both groups (P>0.05). High-pitch helical CTPA acquired during BH or in FB yields comparable image quality for the diagnosis of PE and lung pathology, with low radiation exposure. Only a modest increase in lung parenchymal artifacts is encountered in FB high-pitch helical CTPA.

Adaptive Radiation Therapy for Localized Mesothelioma with Mediastinal Metastasis Using Helical Tomotherapy

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

Renaud, James; Yartsev, Slav; Department of Oncology, University of Western Ontario, London, Ontario

2009-10-01

The purpose of this study was to compare 2 adaptive radiotherapy strategies with helical tomotherapy. A patient having mesothelioma with mediastinal nodes was treated using helical tomotherapy with pretreatment megavoltage CT (MVCT) imaging. Gross tumor volumes (GTVs) were outlined on every MVCT study. Two alternatives for adapting the treatment were investigated: (1) keeping the prescribed dose to the targets while reducing the dose to the OARs and (2) escalating the target dose while maintaining the original level of healthy tissue sparing. Intensity modulated radiotherapy (step-and-shoot IMRT) and 3D conformal radiotherapy (3DCRT) plans for the patient were generated and compared. Themore » primary lesion and nodal mass regressed by 16.2% and 32.5%, respectively. Adapted GTVs and reduced planning target volume (PTV) margins of 4 mm after 22 fractions decrease the planned mean lung dose by 19.4%. For dose escalation, the planned prescribed doses may be increased from 50.0 to 58.7 Gy in PTV{sub 1} and from 60.0 to 70.5 Gy in PTV{sub 2}. The step-and-shoot IMRT plan was better in sparing healthy tissue but did not provide target coverage as well as the helical tomotherapy plan. The 3DCRT plan resulted in a prohibitively high planned dose to the spinal cord. MVCT studies provide information both for setup correction and plan adaptation. Improved healthy tissue sparing and/or dose escalation can be achieved by adaptive planning.« less

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.

MBAR-enhanced lattice Monte Carlo simulation of the effect of helices on membrane protein aggregation

NASA Astrophysics Data System (ADS)

Xu, Yuanwei; Rodger, P. Mark

2017-03-01

We study the effect of helical structure on the aggregation of proteins using a simplified lattice protein model with an implicit membrane environment. A recently proposed Monte Carlo approach, which exploits the proven statistical optimality of the MBAR estimator in order to improve simulation efficiency, was used. The results show that with both two and four proteins present, the tendency to aggregate is strongly expedited by the presence of amphipathic helix (APH), whereas a transmembrane helix (TMH) slightly disfavours aggregation. When four protein molecules are present, partially aggregated states (dimers and trimers) were more common when the APH was present, compared with the cases where no helices or only the TMH is present.

Validation of single-fluid and two-fluid magnetohydrodynamic models of the helicity injected torus spheromak experiment with the NIMROD code

NASA Astrophysics Data System (ADS)

Akcay, Cihan; Kim, Charlson C.; Victor, Brian S.; Jarboe, Thomas R.

2013-08-01

We present a comparison study of 3-D pressureless resistive MHD (rMHD) and 3-D presureless two-fluid MHD models of the Helicity Injected Torus with Steady Inductive helicity injection (HIT-SI). HIT-SI is a current drive experiment that uses two geometrically asymmetric helicity injectors to generate and sustain toroidal plasmas. The comparable size of the collisionless ion skin depth di to the resistive skin depth predicates the importance of the Hall term for HIT-SI. The simulations are run with NIMROD, an initial-value, 3-D extended MHD code. The modeled plasma density and temperature are assumed uniform and constant. The helicity injectors are modeled as oscillating normal magnetic and parallel electric field boundary conditions. The simulations use parameters that closely match those of the experiment. The simulation output is compared to the formation time, plasma current, and internal and surface magnetic fields. Results of the study indicate 2fl-MHD shows quantitative agreement with the experiment while rMHD only captures the qualitative features. The validity of each model is assessed based on how accurately it reproduces the global quantities as well as the temporal and spatial dependence of the measured magnetic fields. 2fl-MHD produces the current amplification Itor/Iinj and formation time τf demonstrated by HIT-SI with similar internal magnetic fields. rMHD underestimates Itor/Iinj and exhibits much a longer τf. Biorthogonal decomposition (BD), a powerful mathematical tool for reducing large data sets, is employed to quantify how well the simulations reproduce the measured surface magnetic fields without resorting to a probe-by-probe comparison. BD shows that 2fl-MHD captures the dominant surface magnetic structures and the temporal behavior of these features better than rMHD.

A Sun-to-Earth Analysis of Magnetic Helicity of the 2013 March 17–18 Interplanetary Coronal Mass Ejection

NASA Astrophysics Data System (ADS)

Pal, Sanchita; Gopalswamy, Nat; Nandy, Dibyendu; Akiyama, Sachiko; Yashiro, Seiji; Makela, Pertti; Xie, Hong

2017-12-01

We compare the magnetic helicity in the 2013 March 17–18 interplanetary coronal mass ejection (ICME) flux rope at 1 au and in its solar counterpart. The progenitor coronal mass ejection (CME) erupted on 2013 March 15 from NOAA active region 11692 and is associated with an M1.1 flare. We derive the source region reconnection flux using the post-eruption arcade (PEA) method that uses the photospheric magnetogram and the area under the PEA. The geometrical properties of the near-Sun flux rope is obtained by forward-modeling of white-light CME observations. Combining the geometrical properties and the reconnection flux, we extract the magnetic properties of the CME flux rope. We derive the magnetic helicity of the flux rope using its magnetic and geometric properties obtained near the Sun and at 1 au. We use a constant-α force-free cylindrical flux rope model fit to the in situ observations in order to derive the magnetic and geometric information of the 1 au ICME. We find a good correspondence in both amplitude and sign of the helicity between the ICME and the CME, assuming a semi-circular (half torus) ICME flux rope with a length of π au. We find that about 83% of the total flux rope helicity at 1 au is injected by the magnetic reconnection in the low corona. We discuss the effect of assuming flux rope length in the derived value of the magnetic helicity. This study connecting the helicity of magnetic flux ropes through the Sun–Earth system has important implications for the origin of helicity in the interplanetary medium and the topology of ICME flux ropes at 1 au and hence their space weather consequences.

Triple-phase helical computed tomography in dogs with solid splenic masses

PubMed Central

KUTARA, Kenji; SEKI, Mamiko; ISHIGAKI, Kumiko; TESHIMA, Kenji; ISHIKAWA, Chieko; KAGAWA, Yumiko; EDAMURA, Kazuya; NAKAYAMA, Tomohiro; ASANO, Kazushi

2017-01-01

We investigated the utility of triple-phase helical computed tomography (CT) in differentiating between benign and malignant splenic masses in dogs. Forty-two dogs with primary splenic masses underwent triple-phase helical CT scanning (before administration of contrast, and in the arterial phase, portal venous phase, and delayed phase) prior to splenectomy. Tissue specimens were sent for pathological diagnosis; these included hematomas (n=14), nodular hyperplasias (n=12), hemangiosarcomas (n=11), and undifferentiated sarcomas (n=5). The CT findings were compared with the histological findings. Nodular hyperplasia significantly displayed a homogeneous normal enhancement pattern in all phases. Hemangiosarcoma displayed 2 significant contrast-enhancement patterns, including a homogeneous pattern of poor enhancement in all phases, and a heterogeneous remarkable enhancement pattern in the arterial and portal venous phases. Hematoma and undifferentiated sarcoma displayed a heterogeneous normal enhancement pattern in all phases. The contrast-enhanced volumetric ratios of hematoma tended to be greater than those of undifferentiated sarcoma. Our study demonstrated that the characteristic findings on triple-phase helical CT could be useful for the preoperative differentiation of hematoma, nodular hyperplasia, hemangiosarcoma, and undifferentiated sarcoma in dogs. Triple-phase helical CT may be a useful diagnostic tool in dogs with splenic masses. PMID:28993600

Effect of Relative Marker Movement on the Calculation of the Foot Torsion Axis Using a Combined Cardan Angle and Helical Axis Approach

PubMed Central

Graf, Eveline S.; Wright, Ian C.; Stefanyshyn, Darren J.

2012-01-01

The two main movements occurring between the forefoot and rearfoot segment of a human foot are flexion at the metatarsophalangeal joints and torsion in the midfoot. The location of the torsion axis within the foot is currently unknown. The purpose of this study was to develop a method based on Cardan angles and the finite helical axis approach to calculate the torsion axis without the effect of flexion. As the finite helical axis method is susceptible to error due to noise with small helical rotations, a minimal amount of rotation was defined in order to accurately determine the torsion axis location. Using simulation, the location of the axis based on data containing noise was compared to the axis location of data without noise with a one-sample t-test and Fisher's combined probability score. When using only data with helical rotation of seven degrees or more, the location of the torsion axis based on the data with noise was within 0.2 mm of the reference location. Therefore, the proposed method allowed an accurate calculation of the foot torsion axis location. PMID:22666303

Enhanced performance of core-shell structured polyaniline at helical carbon nanotube hybrids for ammonia gas sensor

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

Tian, Xin; Wang, Qiang; Chen, Xiangnan

2014-11-17

A core-shell structured hybrid of polyaniline at helical carbon nanotubes was synthesized using in situ polymerization, which the helical carbon nanotubes were uniformly surrounded by a layer of polyaniline nanorods array. More interestingly, repeatable responses were experimentally observed that the sensitivity to ammonia gas of the as-prepared helical shaped core-shell hybrid displays an enhancement of more than two times compared to those of only polyaniline or helical carbon nanotubes sensors because of the peculiar structures with high surface area. This kind of hybrid comprising nanorod arrays of conductive polymers covering carbon nanotubes and related structures provide a potential in sensorsmore » of trace gas detection for environmental monitoring and safety forecasting.« less

Procedure for measuring photon and vector meson circular polarization variation with respect to the reaction plane in relativistic heavy-ion collisions

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

Tang, A. H.; Wang, G.

The electromagnetic (EM) eld pattern created by spectators in relativistic heavy-ion collisions plants a seed of positive (negative) magnetic helicity in the hemisphere above (below) the reaction plane. Owing to the chiral anomaly, the magnetic helicity interacts with the fermionic helicity of the collision system, and causes photons emitted in upper- and lower-hemispheres to have different preferences in the circular polarization. Similar helicity separation for massive particles, due to the global vorticity, is also possible. In this paper, we lay down a procedure to measure the variation of the circular polarization w.r.t the reaction plane in relativistic heavy-ion collisions formore » massless photons, as well as similar polarization patterns for vector mesons decaying into two daughters. We propose to study the yield differentially and compare the yield between upper- and lower-hemispheres in order to identify and quantify such effects.« less

Procedure for measuring photon and vector meson circular polarization variation with respect to the reaction plane in relativistic heavy-ion collisions

DOE PAGES

Tang, A. H.; Wang, G.

2016-08-30

The electromagnetic (EM) eld pattern created by spectators in relativistic heavy-ion collisions plants a seed of positive (negative) magnetic helicity in the hemisphere above (below) the reaction plane. Owing to the chiral anomaly, the magnetic helicity interacts with the fermionic helicity of the collision system, and causes photons emitted in upper- and lower-hemispheres to have different preferences in the circular polarization. Similar helicity separation for massive particles, due to the global vorticity, is also possible. In this paper, we lay down a procedure to measure the variation of the circular polarization w.r.t the reaction plane in relativistic heavy-ion collisions formore » massless photons, as well as similar polarization patterns for vector mesons decaying into two daughters. We propose to study the yield differentially and compare the yield between upper- and lower-hemispheres in order to identify and quantify such effects.« less

Sustainment Study of Flipped Spherical Torus Plasmas on HIST

NASA Astrophysics Data System (ADS)

Takamiya, T.; Nagata, M.; Kawami, K.; Hasegawa, H.; Fukumoto, N.; Uyama, T.; Masamune, S.; Iida, M.; Katsurai, M.

2003-10-01

We have discovered that helicity-driven ST plasmas relax toward the flipped state by decreasing the external toroidal field and reversing its sign in time [1]. From the viewpoint of coaxial helicity injection (CHI) current drive, it is conceivable that the flipped ST (F-ST), which consists of only closed flux surfaces, compares favorably with the normal ST. We have investigated the sustainment mechanism of the F-ST plasma. The helicity-driven relaxed theory shows that there exist the mixed states of ST and F-ST in the flux conserver. Helicity is transferred to F-ST through the ST with coupling with gun electrodes. It has been found that magnetic reconnection between the toroidal magnetic field plays important role in the sustainment of the F-ST. The magnetic field in the outer edge region shows regular oscillations which have a large amplitude of the n=1 mode. The core region of the F-ST seems to be relatively stable. [1] M. Nagata, et al., Phys. Rev. Lett. 90, 225001 (2003)

BASIC BIOCHEMICAL AND CLINICAL ASPECTS OF NONINVASIVE TESTS HELIC.

PubMed

Dmitrienko, M A; Dmitrienko, V S; Kornienko, E A; Parolova, N I; Colomina, E O; Aronov, E B

Biochemical process that lay in the core of non-invasive detection of Helico ho cter pylod with the help of HELIC Ammonia breath test, manufactured by AMA Co Ltd., St.Petersburg, is shown. Patents from various countries, describing ammonia as H.pyiori diagnostic marker, are reviewed. Approaches for evaluation of efficacy of the test-system are analyzed, validation and verification data is provided. High diagnostic characteristics are confirmed by the results of comparative studies on patients of different age groups, reaching 97% sensitivity and 96% specificity.

Thermodynamic and structural effect of urea and guanidine chloride on the helical and on a hairpin fragment of GB1 from molecular simulations.

PubMed

Meloni, R; Tiana, G

2017-04-01

With the help of molecular-dynamics simulations, we studied the effect of urea and guanidine chloride on the thermodynamic and structural properties of the helical fragment of protein GB1, comparing them with those of its second beta hairpin. We showed that the helical fragment in different solvents populates an ensemble of states that is more complex than that of the hairpin, and thus the associated experimental observables (circular-dichroism spectra, secondary chemical shifts, m values), that we back-calculated from the simulations and compared with the actual data, are more difficult to interpret. We observed that in the case of both peptides, urea binds tightly to their backbone, while guanidine exerts its denaturing effect in a more subtle way, strongly affecting the electrostatic properties of the solution. This difference can have consequences in the way denaturation experiments are interpreted. Proteins 2017; 85:753-763. © 2016 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

High temperature helical tubular receiver for concentrating solar power system

NASA Astrophysics Data System (ADS)

Hossain, Nazmul

In the field of conventional cleaner power generation technology, concentrating solar power systems have introduced remarkable opportunity. In a solar power tower, solar energy concentrated by the heliostats at a single point produces very high temperature. Falling solid particles or heat transfer fluid passing through that high temperature region absorbs heat to generate electricity. Increasing the residence time will result in more heat gain and increase efficiency. A novel design of solar receiver for both fluid and solid particle is approached in this paper which can increase residence time resulting in higher temperature gain in one cycle compared to conventional receivers. The helical tubular solar receiver placed at the focused sunlight region meets the higher outlet temperature and efficiency. A vertical tubular receiver is modeled and analyzed for single phase flow with molten salt as heat transfer fluid and alloy625 as heat transfer material. The result is compared to a journal paper of similar numerical and experimental setup for validating our modeling. New types of helical tubular solar receivers are modeled and analyzed with heat transfer fluid turbulent flow in single phase, and granular particle and air plug flow in multiphase to observe the temperature rise in one cyclic operation. The Discrete Ordinate radiation model is used for numerical analysis with simulation software Ansys Fluent 15.0. The Eulerian granular multiphase model is used for multiphase flow. Applying the same modeling parameters and boundary conditions, the results of vertical and helical receivers are compared. With a helical receiver, higher temperature gain of heat transfer fluid is achieved in one cycle for both single phase and multiphase flow compared to the vertical receiver. Performance is also observed by varying dimension of helical receiver.

Helical and rod-shaped bacteria swim in helical trajectories with little additional propulsion from helical shape

NASA Astrophysics Data System (ADS)

Fu, Henry; Constantino, Maira; Jabbarzadeh, Mehdi; Bansil, Rama

2017-11-01

It has frequently been hypothesized that the helical body shapes of flagellated bacteria may yield some advantage in swimming ability. The helical-shaped pathogen Helicobacter pylori allows us to test these claims. Using fast time-resolution and high-magnification phase-contrast microscopy to simultaneously image and track individual bacteria we determine cell body shape as well as rotational and translational speeds. Using the method of regularized Stokeslets, we directly compare observed speeds and trajectories to numerical calculations to validate the numerical model. Although experimental observations are limited to select cases, the model allows quantification of the effects of body helicity, length, and diameter. We find that due to relatively slow body rotation rates, the helical shape makes at most a 15% contribution to propulsive thrust. The effect of body shape on swimming speeds is instead dominated by variations in translational drag required to move the cell body. Because helical cells are one of the strongest candidates for propulsion arising from the cell body, our results imply that quite generally, swimming speeds of flagellated bacteria can only be increased a little by by body propulsion.

Comparison of performance of shell-and-tube heat exchangers with conventional segmental baffles and continuous helical baffle

NASA Astrophysics Data System (ADS)

Ahmed, Asif; Ferdous, Imam Ul.; Saha, Sumon

2017-06-01

In the present study, three-dimensional numerical simulation of two shell-and-tube heat exchangers (STHXs) with conventional segmental baffles (STHXsSB) and continuous helical baffle (STHXsHB) is carried out and a comparative study is performed based on the simulation results. Both of the STHXs contain 37 tubes inside a 500 mm long and 200 mm diameter shell and mass flow rate of shell-side fluid is varied from 0.5 kg/s to 2 kg/s. At first, physical and mathematical models are developed and numerically simulated using finite element method (FEM). For the validation of the computational model, shell-side average nusselt number (Nus) is calculated from the simulation results and compared with the available experimental results. The comparative study shows that STHXsHB has 72-127% higher heat transfer coefficient per unit pressure drop compared to the conventional STHXsSB for the same shell-side mass flow rate. Moreover, STHXsHB has 59-63% lower shell-side pressure drop than STHXsSB.

Comparative divertor-transport study for helical devices

NASA Astrophysics Data System (ADS)

Feng, Y.; Kobayashi, M.; Sardei, F.; Masuzaki, S.; Kisslinger, J.; Morisaki, T.; Grigull, P.; Yamada, H.; McCormick, K.; Ohyabu, N.; König, R.; Yamada, I.; Giannone, L.; Narihara, K.; Wenzel, U.; Morita, S.; Thomsen, H.; Miyazawa, J.; Hildebrandt, D.; Watanabe, T.; Wagner, F.; Ashikawa, N.; Ida, K.; Komori, A.; Motojima, O.; Nakamura, Y.; Peterson, B. J.; Sato, K.; Shoji, M.; Tamura, N.; Tokitani, M.; LHD experimental Group

2009-09-01

Using the island divertors (IDs) of W7-AS and W7-X and the helical divertor (HD) of LHD as examples, the paper presents a comparative divertor transport study for three typical helical devices of different machine sizes following two distinct divertor concepts, aiming at identifying common physics issues/effects for mutual validation and combined studies. Based on EMC3/EIRENE simulations supported by experimental results, the paper first reviews and compares the essential transport features of the W7-AS ID and the LHD HD in order to build a base and framework for a predictive study of W7-X. The fundamental role of low-order magnetic islands in both divertor concepts is emphasized. Preliminary EMC3/EIRENE simulation results for W7-X are presented and discussed with respect to W7-AS and LHD in order to show how the individual field and divertor topologies affect the divertor transport and performance. For instance, a high recycling regime, which is absent from W7-AS and LHD, is predicted to exist for W7-X. The paper focuses on identifying and understanding the role of divertors for high density plasma operations in helical devices. In this regard, special attention is paid to investigating the divertor function for controlling intrinsic impurities. Impurity transport behaviour and wall-sputtering processes of CX-neutrals are studied under different divertor plasma conditions. A divertor retention effect on intrinsic impurities at high SOL collisonalities is predicted for all the three devices. The required SOL plasma conditions and the underlying mechanisms are analysed in detail. Numerical results are discussed in conjunction with the experimental observations for high density divertor plasmas in W7-AS and LHD. Different SOL transport regimes are numerically identified for the standard divertor configuration of W7-X and the possible consequences on high density plasmas are assessed. All the EMC3-EIRENE simulations presented in this paper are based on vacuum fields and comparisons with local diagnostics are made for low-ß plasmas.

Magnetic design constraints of helical solenoids

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

Lopes, M. L.; Krave, S. T.; Tompkins, J. C.

2015-01-30

Helical solenoids have been proposed as an option for a Helical Cooling Channel for muons in a proposed Muon Collider. Helical solenoids can provide the required three main field components: solenoidal, helical dipole, and a helical gradient. In general terms, the last two are a function of many geometric parameters: coil aperture, coil radial and longitudinal dimensions, helix period and orbit radius. In this paper, we present design studies of a Helical Solenoid, addressing the geometric tunability limits and auxiliary correction system.

Magnetic helicity balance at Taylor relaxed states sustained by AC helicity injection

NASA Astrophysics Data System (ADS)

Hirota, Makoto; Morrison, Philip J.; Horton, Wendell; Hattori, Yuji

2017-10-01

Magnitudes of Taylor relaxed states that are sustained by AC magnetic helicity injection (also known as oscillating field current drive, OFCD) are investigated numerically in a cylindrical geometry. Compared with the amplitude of the oscillating magnetic field at the skin layer (which is normalized to 1), the strength of the axial guide field Bz 0 is shown to be an important parameter. The relaxation process seems to be active only when Bz 0 < 1 . Moreover, in the case of weak guide field Bz 0 < 0.2 , a helically-symmetric relaxed state is self-generated instead of the axisymmetric reversed-field pinch. As a theoretical model, the helicity balance is considered in a similar way to R. G. O'Neill et al., where the helicity injection rate is directly equated with the dissipation rate at the Taylor states. Then, the bifurcation to the helical Taylor state is predicted theoretically and the estimated magnitudes of the relaxed states reasonably agree with numerical results as far as Bz 0 < 1 . This work was supported by JSPS KAKENHI Grant Number 16K05627.

Helical and rod-shaped bacteria swim in helical trajectories with little additional propulsion from helical shape

PubMed Central

Constantino, Maira A.; Jabbarzadeh, Mehdi; Fu, Henry C.; Bansil, Rama

2016-01-01

It has frequently been hypothesized that the helical body shapes of flagellated bacteria may yield some advantage in swimming ability. In particular, the helical-shaped pathogen Helicobacter pylori is often claimed to swim like a corkscrew through its harsh gastric habitat, but there has been no direct confirmation or quantification of such claims. Using fast time-resolution and high-magnification two-dimensional (2D) phase-contrast microscopy to simultaneously image and track individual bacteria in bacterial broth as well as mucin solutions, we show that both helical and rod-shaped H. pylori rotated as they swam, producing a helical trajectory. Cell shape analysis enabled us to determine shape as well as the rotational and translational speed for both forward and reverse motions, thereby inferring flagellar kinematics. Using the method of regularized Stokeslets, we directly compare observed speeds and trajectories to numerical calculations for both helical and rod-shaped bacteria in mucin and broth to validate the numerical model. Although experimental observations are limited to select cases, the model allows quantification of the effects of body helicity, length, and diameter. We find that due to relatively slow body rotation rates, the helical shape makes at most a 15% contribution to propulsive thrust. The effect of body shape on swimming speeds is instead dominated by variations in translational drag required to move the cell body. Because helical cells are one of the strongest candidates for propulsion arising from the cell body, our results imply that quite generally, swimming speeds of flagellated bacteria can only be increased a little by body propulsion. PMID:28138539

On the inverse transfer of (non-)helical magnetic energy in a decaying magnetohydrodynamic turbulence

NASA Astrophysics Data System (ADS)

Park, Kiwan

2017-12-01

In our conventional understanding, large-scale magnetic fields are thought to originate from an inverse cascade in the presence of magnetic helicity, differential rotation or a magneto-rotational instability. However, as recent simulations have given strong indications that an inverse cascade (transfer) may occur even in the absence of magnetic helicity, the physical origin of this inverse cascade is still not fully understood. We here present two simulations of freely decaying helical and non-helical magnetohydrodynamic (MHD) turbulence. We verified the inverse transfer of helical and non-helical magnetic fields in both cases, but we found the underlying physical principles to be fundamentally different. In the former case, the helical magnetic component leads to an inverse cascade of magnetic energy. We derived a semi-analytic formula for the evolution of large-scale magnetic field using α coefficient and compared it with the simulation data. But in the latter case, the α effect, including other conventional dynamo theories, is not suitable to describe the inverse transfer of non-helical magnetic energy. To obtain a better understanding of the physics at work here, we introduced a 'field structure model' based on the magnetic induction equation in the presence of inhomogeneities. This model illustrates how the curl of the electromotive force leads to the build up of a large-scale magnetic field without the requirement of magnetic helicity. And we applied a quasi-normal approximation to the inverse transfer of magnetic energy.

Advanced Face Gear Surface Durability Evaluations

NASA Technical Reports Server (NTRS)

Lewicki, David G.; Heath, Gregory F.

2016-01-01

The surface durability life of helical face gears and isotropic super-finished (ISF) face gears was investigated. Experimental fatigue tests were performed at the NASA Glenn Research Center. Endurance tests were performed on 10 sets of helical face gears in mesh with tapered involute helical pinions, and 10 sets of ISF-enhanced straight face gears in mesh with tapered involute spur pinions. The results were compared to previous tests on straight face gears. The life of the ISF configuration was slightly less than that of previous tests on straight face gears. The life of the ISF configuration was slightly greater than that of the helical configuration.

Evolution of relative magnetic helicity. New boundary conditions for the vector potential

NASA Astrophysics Data System (ADS)

Yang, Shangbin; Büchner, Jörg; Skála, Jan; Zhang, Hongqi

2018-05-01

Context. For a better understanding of the dynamics of the solar corona, it is important to analyse the evolution of the helicity of the magnetic field. Since the helicity cannot be directly determined by observations, we have recently proposed a method to calculate the relative magnetic helicity in a finite volume for a given magnetic field, which however required the flux to be balanced separately on all the sides of the considered volume. Aims: We developed a scheme to obtain the vector potential in a volume without the above restriction at the boundary. We studied the dissipation and escape of relative magnetic helicity from an active region. Methods: In order to allow finite magnetic fluxes through the boundaries, a Coulomb gauge was constructed that allows for global magnetic flux balance. The property of sinusoidal function was used to obtain the vector potentials at the 12 edges of the considered rectangular volume extending above an active region. We tested and verified our method in a theoretical fore-free magnetic field model. Results: We applied the new method to the former calculation data and found a difference of less than 1.2%. We also applied our method to the magnetic field above active region NOAA 11429 obtained by a new photospheric-data-driven magnetohydrodynamics (MHD) model code GOEMHD3. We analysed the magnetic helicity evolution in the solar corona using our new method. We find that the normalized magnetic helicity (H/Φ2) is equal to -0.038 when fast magnetic reconnection is triggered. This value is comparable to the previous value (-0.029) in the MHD simulations when magnetic reconnection happened and the observed normalized magnetic helicity (-0.036) from the eruption of newly emerging active regions. We find that only 8% of the accumulated magnetic helicity is dissipated after it is injected through the bottom boundary. This is in accordance with the Woltjer conjecture. Only 2% of the magnetic helicity injected from the bottom boundary escapes through the corona. This is consistent with the observation of magnetic clouds, which could take magnetic helicity into the interplanetary space. In the case considered here, several halo coronal mass ejections (CMEs) and two X-class solar flares originate from this active region.

Effects of number and configuration of flagella on motility of Helicobacter species.

NASA Astrophysics Data System (ADS)

Constantino, Maira A.; Sharba, Sinan; Shen, Zeli; Fox, James G.; Haesebrouck, Freddy; Linden, Sara; Bansil, Rama

Helicobacters are ulcer-causing bacteria that colonize the viscoelastic gastric mucus layer of mammals. Previous studies have shown that motility and colonization are affected by helical body shape, number and configuration of flagella. In a recent study, using fast time-resolution and high-magnification 2-D phase-contrast microscopy to image individual helical and rod-shaped H. pylori we measured the rotation rate of the cell body and flagella and found that helical shape produces less than 15% changes in swimming speeds as compared to the rod-shaped cell. Motility of H. pylori was strongly influenced by its multiple unipolar flagella. Here we compare rotational and translational speeds of H. cetorum and H. suis which have bipolar flagella, with H. cetorum having single bipolar flagella and H. suis having multiple flagella. Preliminary results show that H. suis bacteria swim slower but rotate at the same rate as H. pylori and present two swimming modes. It can swim as a pusher, with one active rotating bundle and one inactive bundle, wrapped around the body or with both bundles active. Similar work on H. cetorum is ongoing and will also be presented. NSF PHY 1410798.

Evidence for α-helices in the gas phase: a case study using Melittin from honey bee venom.

PubMed

Florance, Hannah V; Stopford, Andrew P; Kalapothakis, Jason M; McCullough, Bryan J; Bretherick, Andrew; Barran, Perdita E

2011-09-07

Gas phase methodologies are increasingly used to study the structure of proteins and peptides. A challenge to the mass spectrometrist is to preserve the structure of the system of interest intact and unaltered from solution into the gas phase. Small peptides are very flexible and can present a number of conformations in solution. In this work we examine Melittin a 26 amino acid peptide that forms the active component of honey bee venom. Melittin is haemolytic and has been shown to form an α-helical tetrameric structure by X-ray crystallography [M. Gribskov et al., The RCSB Protein Data Bank, 1990] and to be helical in high concentrations of methanol. Here we use ion mobility mass spectrometry, molecular dynamics and gas-phase HDX to probe its structure in the gas phase and specifically interrogate whether the helical form can be preserved. All low energy calculated structures possess some helicity. In our experiments we examine the peptide following nano-ESI from solutions with varying methanol content. Ion mobility gives collision cross sections (CCS) that compare well with values found from molecular modelling and from other reported structures, but with inconclusive results regarding the effect of solvent. There is only a slight increase in CCS with charge, showing minimal coloumbically driven unfolding. HDX supports preservation of some helical content into the gas phase and again shows little difference in the exchange rates of species sprayed from different solvents. The [M + 3H](3+) species has two exchanging populations both of which exhibit faster exchange rates than observed for the [M + 2H](2+) species. One interpretation for these results is that the time spent being analysed is sufficient for this peptide to form a helix in the 'ultimate' hydrophobic environment of a vacuum.

Validation of an Accurate Three-Dimensional Helical Slow-Wave Circuit Model

NASA Technical Reports Server (NTRS)

Kory, Carol L.

1997-01-01

The helical slow-wave circuit embodies a helical coil of rectangular tape supported in a metal barrel by dielectric support rods. Although the helix slow-wave circuit remains the mainstay of the traveling-wave tube (TWT) industry because of its exceptionally wide bandwidth, a full helical circuit, without significant dimensional approximations, has not been successfully modeled until now. Numerous attempts have been made to analyze the helical slow-wave circuit so that the performance could be accurately predicted without actually building it, but because of its complex geometry, many geometrical approximations became necessary rendering the previous models inaccurate. In the course of this research it has been demonstrated that using the simulation code, MAFIA, the helical structure can be modeled with actual tape width and thickness, dielectric support rod geometry and materials. To demonstrate the accuracy of the MAFIA model, the cold-test parameters including dispersion, on-axis interaction impedance and attenuation have been calculated for several helical TWT slow-wave circuits with a variety of support rod geometries including rectangular and T-shaped rods, as well as various support rod materials including isotropic, anisotropic and partially metal coated dielectrics. Compared with experimentally measured results, the agreement is excellent. With the accuracy of the MAFIA helical model validated, the code was used to investigate several conventional geometric approximations in an attempt to obtain the most computationally efficient model. Several simplifications were made to a standard model including replacing the helical tape with filaments, and replacing rectangular support rods with shapes conforming to the cylindrical coordinate system with effective permittivity. The approximate models are compared with the standard model in terms of cold-test characteristics and computational time. The model was also used to determine the sensitivity of various circuit parameters including typical manufacturing dimensional tolerances and support rod permittivity. By varying the circuit parameters of an accurate model using MAFIA, these sensitivities can be computed for manufacturing concerns, and design optimization previous to fabrication, thus eliminating the need for costly experimental iterations. Several variations were made to a standard helical circuit using MAFIA to investigate the effect that variations on helical tape and support rod width, metallized loading height and support rod permittivity, have on TWT cold-test characteristics.

On the resilience of helical magnetic fields to turbulent diffusion and the astrophysical implications

NASA Astrophysics Data System (ADS)

Blackman, Eric G.; Subramanian, Kandaswamy

2013-02-01

The extent to which large-scale magnetic fields are susceptible to turbulent diffusion is important for interpreting the need for in situ large-scale dynamos in astrophysics and for observationally inferring field strengths compared to kinetic energy. By solving coupled evolution equations for magnetic energy and magnetic helicity in a system initialized with isotropic turbulence and an arbitrarily helical large-scale field, we quantify the decay rate of the latter for a bounded or periodic system. The magnetic energy associated with the non-helical large-scale field decays at least as fast as the kinematically estimated turbulent diffusion rate, but the decay rate of the helical part depends on whether the ratio of its magnetic energy to the turbulent kinetic energy exceeds a critical value given by M1, c = (k1/k2)2, where k1 and k2 are the wavenumbers of the large and forcing scales. Turbulently diffusing helical fields to small scales while conserving magnetic helicity requires a rapid increase in total magnetic energy. As such, only when the helical field is subcritical can it so diffuse. When supercritical, it decays slowly, at a rate determined by microphysical dissipation even in the presence of macroscopic turbulence. In effect, turbulent diffusion of such a large-scale helical field produces small-scale helicity whose amplification abates further turbulent diffusion. Two curious implications are that (1) standard arguments supporting the need for in situ large-scale dynamos based on the otherwise rapid turbulent diffusion of large-scale fields require re-thinking since only the large-scale non-helical field is so diffused in a closed system. Boundary terms could however provide potential pathways for rapid change of the large-scale helical field. (2) Since M1, c ≪ 1 for k1 ≪ k2, the presence of long-lived ordered large-scale helical fields as in extragalactic jets do not guarantee that the magnetic field dominates the kinetic energy.

Effect of helicity on the correlation time of large scales in turbulent flows

NASA Astrophysics Data System (ADS)

Cameron, Alexandre; Alexakis, Alexandros; Brachet, Marc-Étienne

2017-11-01

Solutions of the forced Navier-Stokes equation have been conjectured to thermalize at scales larger than the forcing scale, similar to an absolute equilibrium obtained for the spectrally truncated Euler equation. Using direct numeric simulations of Taylor-Green flows and general-periodic helical flows, we present results on the probability density function, energy spectrum, autocorrelation function, and correlation time that compare the two systems. In the case of highly helical flows, we derive an analytic expression describing the correlation time for the absolute equilibrium of helical flows that is different from the E-1 /2k-1 scaling law of weakly helical flows. This model predicts a new helicity-based scaling law for the correlation time as τ (k ) ˜H-1 /2k-1 /2 . This scaling law is verified in simulations of the truncated Euler equation. In simulations of the Navier-Stokes equations the large-scale modes of forced Taylor-Green symmetric flows (with zero total helicity and large separation of scales) follow the same properties as absolute equilibrium including a τ (k ) ˜E-1 /2k-1 scaling for the correlation time. General-periodic helical flows also show similarities between the two systems; however, the largest scales of the forced flows deviate from the absolute equilibrium solutions.

Global-Scale Consequences of Magnetic-Helicity Injection and Condensation on the Sun

NASA Technical Reports Server (NTRS)

Mackay, Duncan H.; DeVore, C. Richard; Antiochos, Spiro K.

2013-01-01

In the recent paper of Antiochos, a new concept for the injection of magnetic helicity into the solar corona by small-scale convective motions and its condensation onto polarity inversion lines (PILs) has been developed. We investigate this concept through global simulations of the Sun's photospheric and coronal magnetic fields and compare the results with the hemispheric pattern of solar filaments. Assuming that the vorticity of the cells is predominately counter-clockwise/clockwise in the northern/southern hemisphere, the convective motions inject negative/positive helicity into each hemisphere. The simulations show that: (i) On a north-south orientated PIL, both differential rotation and convective motions inject the same sign of helicity which matches that required to reproduce the hemispheric pattern of filaments. (ii) On a high latitude east-west orientated polar crown or sub-polar crown PIL, the vorticity of the cells has to be approximately 2-3 times greater than the local differential rotation gradient in order to overcome the incorrect sign of helicity injection from differential rotation. (iii) In the declining phase of the cycle, as a bipole interacts with the polar field, in some cases helicity condensation can reverse the effect of differential rotation along the East-West lead arm, but not in all cases. The results show that this newly developed concept of magnetic helicity injection and condensation is a viable method to explain the hemispheric pattern of filaments in conjunction with the mechanisms used in Yeates et al. (2008). Future observational studies should focus on determining the vorticity component within convective motions to determine, both its magnitude and latitudinal variation relative to the differential rotation gradient on the Sun.

Analysis of peripheral doses for base of tongue treatment by linear accelerator and helical TomoTherapy IMRT

PubMed Central

Lamba, Michael A. S.; Elson, Howard R.

2010-01-01

The purpose of this study was to compare the peripheral doses to various organs from a typical head and neck intensity‐modulated radiation therapy (IMRT) treatment delivered by linear accelerator (linac) and helical TomoTherapy. Multiple human CT data sets were used to segment critical structures and organs at risk, fused and adjusted to an anthropomorphic phantom. Eighteen contours were designated for thermoluminescent dosimeter (TLD) placement. Following the RTOG IMRT Protocol 0522, treatment of the primary tumor and involved nodes (PTV70) and subclinical disease sites (PTV56) was planned utilizing IMRT to 70 Gy and 56 Gy. Clinically acceptable treatment plans were produced for linac and TomoTherapy treatments. TLDs were placed and each treatment plan was delivered to the anthropomorphic phantom four times. Within 2.5 cm (one helical TomoTherapy field width) superior and inferior to the field edges, normal tissue doses were on average 45% lower using linear accelerator. Beyond 2.5 cm, the helical TomoTherapy normal tissue dose was an average of 52% lower. The majority of points proved to be statistically different using the Student's t‐test with p<0.05. Using one method of calculation, probability of a secondary malignancy was 5.88% for the linear accelerator and 4.08% for helical TomoTherapy. Helical TomoTherapy delivers more dose than a linac immediately above and below the treatment field, contributing to the higher peripheral doses adjacent to the field. At distances beyond one field width (where leakage is dominant), helical TomoTherapy doses are lower than linear accelerator doses. PACS number: 87.50.cm Dosimetry/exposure assessment

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.

Stabilizing effect of helical current drive on tearing modes

NASA Astrophysics Data System (ADS)

Yuan, Y.; Lu, X. Q.; Dong, J. Q.; Gong, X. Y.; Zhang, R. B.

2018-01-01

The effect of helical driven current on the m = 2/n = 1 tearing mode is studied numerically in a cylindrical geometry using the method of reduced magneto-hydro-dynamic simulation. The results show that the local persistent helical current drive from the beginning time can be applied to control the tearing modes, and will cause a rebound effect called flip instability when the driven current reaches a certain value. The current intensity threshold value for the occurrence of flip instability is about 0.00087I0. The method of controlling the development of tearing mode with comparative economy is given. If the local helical driven current is discontinuous, the magnetic island can be controlled within a certain range, and then, the tearing modes stop growing; thus, the flip instability can be avoided. We also find that the flip instability will become impatient with delay injection of the driven current because the high order harmonics have been developed in the original O-point. The tearing mode instability can be controlled by using the electron cyclotron current drive to reduce the gradient of the current intensity on the rational surfaces.

An experimental study of the flow of LPG as refrigerant inside an adiabatic helical coiled capillary tube in vapour compression refrigeration system

NASA Astrophysics Data System (ADS)

Punia, Sanjeev Singh; Singh, Jagdev

2015-11-01

This paper presents an experimental investigation for the flow of liquefied petroleum gas (LPG) as a refrigerant inside an adiabatic helically coiled capillary tube in vapour compression refrigeration system. The effect of various geometric parameters and operating conditions like capillary tube inner diameter, length of capillary tube, coil diameter and different inlet subcoolings on the mass flow rate of LPG through the helical coiled capillary tube geometry has been investigated. It has been established that the coil diameter significantly influences the mass flow rate of LPG through the adiabatic helical capillary tube. It has been concluded that the effect of coiling of capillary tube reduces the mass flow rate by 5-12 % as compared to those of the straight capillary tube operating under similar conditions. The data obtained from the experiments are analyzed and a dimensionless correlation has been developed. The proposed correlation predicts that more than 90 % of experimental data which is in agreement with measured data in an error band of ±10 %.

Recognizing asymmetry in pseudo-symmetry; structural insights into the interaction between amphipathic α-helices and X-bundle proteins.

PubMed

Haddad, John Faissal; Yang, Yidai; Yeung, Sylvain; Couture, Jean-François

2017-11-01

An α-helix bundle is a small and compact protein fold always composed of more than 2 α-helices that typically run nearly parallel or antiparallel to each other. The repertoire of arrangements of α-helix bundle is such that these domains bind to a myriad of molecular entities including DNA, RNA, proteins and small molecules. A special instance of α-helical bundle is the X-type in which the arrangement of two α-helices interact at 45° to form an X. Among those, some X-helix bundle proteins bind to the hydrophobic section of an amphipathic α-helix in a seemingly orientation and sequence specific manner. In this review, we will compare the binding mode of amphipathic α-helices to X-helix bundle and α-helical bundle proteins. From these structures, we will highlight potential regulatory paradigms that may control the specific interactions of X-helix bundle proteins to amphipathic α-helices. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

Dipole Alignment in Rotating MHD Turbulence

NASA Technical Reports Server (NTRS)

Shebalin, John V.; Fu, Terry; Morin, Lee

2012-01-01

We present numerical results from long-term CPU and GPU simulations of rotating, homogeneous, magnetohydrodynamic (MHD) turbulence, and discuss their connection to the spherically bounded case. We compare our numerical results with a statistical theory of geodynamo action that has evolved from the absolute equilibrium ensemble theory of ideal MHD turbulence, which is based on the ideal MHD invariants are energy, cross helicity and magnetic helicity. However, for rotating MHD turbulence, the cross helicity is no longer an exact invariant, although rms cross helicity becomes quasistationary during an ideal MHD simulation. This and the anisotropy imposed by rotation suggests an ansatz in which an effective, nonzero value of cross helicity is assigned to axisymmetric modes and zero cross helicity to non-axisymmetric modes. This hybrid statistics predicts a large-scale quasistationary magnetic field due to broken ergodicity , as well as dipole vector alignment with the rotation axis, both of which are observed numerically. We find that only a relatively small value of effective cross helicity leads to the prediction of a dipole moment vector that is closely aligned (less than 10 degrees) with the rotation axis. We also discuss the effect of initial conditions, dissipation and grid size on the numerical simulations and statistical theory.

Assessment of temporal resolution of multi-detector row computed tomography in helical acquisition mode using the impulse method.

PubMed

Ichikawa, Katsuhiro; Hara, Takanori; Urikura, Atsushi; Takata, Tadanori; Ohashi, Kazuya

2015-06-01

The purpose of this study was to propose a method for assessing the temporal resolution (TR) of multi-detector row computed tomography (CT) (MDCT) in the helical acquisition mode using temporal impulse signals generated by a metal ball passing through the acquisition plane. An 11-mm diameter metal ball was shot along the central axis at approximately 5 m/s during a helical acquisition, and the temporal sensitivity profile (TSP) was measured from the streak image intensities in the reconstructed helical CT images. To assess the validity, we compared the measured and theoretical TSPs for the 4-channel modes of two MDCT systems. A 64-channel MDCT system was used to compare TSPs and image quality of a motion phantom for the pitch factors P of 0.6, 0.8, 1.0 and 1.2 with a rotation time R of 0.5 s, and for two R/P combinations of 0.5/1.2 and 0.33/0.8. Moreover, the temporal transfer functions (TFs) were calculated from the obtained TSPs. The measured and theoretical TSPs showed perfect agreement. The TSP narrowed with an increase in the pitch factor. The image sharpness of the 0.33/0.8 combination was inferior to that of the 0.5/1.2 combination, despite their almost identical full width at tenth maximum values. The temporal TFs quantitatively confirmed these differences. The TSP results demonstrated that the TR in the helical acquisition mode significantly depended on the pitch factor as well as the rotation time, and the pitch factor and reconstruction algorithm affected the TSP shape. Copyright © 2015 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Validation of single-fluid and two-fluid magnetohydrodynamic models of the helicity injected torus spheromak experiment with the NIMROD code

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

Akcay, Cihan; Victor, Brian S.; Jarboe, Thomas R.

We present a comparison study of 3-D pressureless resistive MHD (rMHD) and 3-D presureless two-fluid MHD models of the Helicity Injected Torus with Steady Inductive helicity injection (HIT-SI). HIT-SI is a current drive experiment that uses two geometrically asymmetric helicity injectors to generate and sustain toroidal plasmas. The comparable size of the collisionless ion skin depth d{sub i} to the resistive skin depth predicates the importance of the Hall term for HIT-SI. The simulations are run with NIMROD, an initial-value, 3-D extended MHD code. The modeled plasma density and temperature are assumed uniform and constant. The helicity injectors are modeledmore » as oscillating normal magnetic and parallel electric field boundary conditions. The simulations use parameters that closely match those of the experiment. The simulation output is compared to the formation time, plasma current, and internal and surface magnetic fields. Results of the study indicate 2fl-MHD shows quantitative agreement with the experiment while rMHD only captures the qualitative features. The validity of each model is assessed based on how accurately it reproduces the global quantities as well as the temporal and spatial dependence of the measured magnetic fields. 2fl-MHD produces the current amplification (I{sub tor}/I{sub inj}) and formation time τ{sub f} demonstrated by HIT-SI with similar internal magnetic fields. rMHD underestimates (I{sub tor}/I{sub inj}) and exhibits much a longer τ{sub f}. Biorthogonal decomposition (BD), a powerful mathematical tool for reducing large data sets, is employed to quantify how well the simulations reproduce the measured surface magnetic fields without resorting to a probe-by-probe comparison. BD shows that 2fl-MHD captures the dominant surface magnetic structures and the temporal behavior of these features better than rMHD.« less

Conceptual Design Study on Bolts for Self-Loosing Preventable Threaded Fasteners

NASA Astrophysics Data System (ADS)

Noma, Atsushi; He, Jianmei

2017-11-01

Threaded fasteners using bolts is widely applied in industrial field as well as various fields. However, threaded fasteners using bolts have loosing problems and cause many accidents. In this study, the purpose is to obtain self-loosing preventable threaded fasteners by applying spring characteristic effects on bolt structures. Helical-cutting applied bolt structures is introduced through three dimensional (3D) CAD modeling tools. Analytical approaches for evaluations on the spring characteristic effects helical-cutting applied bolt structures and self-loosing preventable performance of threaded fasteners were performed using finite element method and results are reported. Comparing slackness test results with analytical results and more details on evaluating mechanical properties will be executed in future study.

Roles of effective helical ripple rates in nonlinear stability of externally induced magnetic islands

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

Nishimura, Seiya, E-mail: n-seiya@kobe-kosen.ac.jp

Magnetic islands are externally produced by resonant magnetic perturbations (RMPs) in toroidal plasmas. Spontaneous annihilation of RMP-induced magnetic islands called self-healing has been observed in helical systems. A possible mechanism of the self-healing is shielding of RMP penetration by helical ripple-induced neoclassical flows, which give rise to neoclassical viscous torques. In this study, effective helical ripple rates in multi-helicity helical systems are revisited, and a multi-helicity effect on the self-healing is investigated, based on a theoretical model of rotating magnetic islands. It is confirmed that effective helical ripple rates are sensitive to magnetic axis positions. It is newly found thatmore » self-healing thresholds also strongly depend on magnetic axis positions, which is due to dependence of neoclassical viscous torques on effective helical ripple rates.« less

Statistical analyses and computational prediction of helical kinks in membrane proteins

NASA Astrophysics Data System (ADS)

Huang, Y.-H.; Chen, C.-M.

2012-10-01

We have carried out statistical analyses and computer simulations of helical kinks for TM helices in the PDBTM database. About 59 % of 1562 TM helices showed a significant kink, and 38 % of these kinks are associated with prolines in a range of ±4 residues. Our analyses show that helical kinks are more populated in the central region of helices, particularly in the range of 1-3 residues away from the helix center. Among 1,053 helical kinks analyzed, 88 % of kinks are bends (change in helix axis without loss of helical character) and 12 % are disruptions (change in helix axis and loss of helical character). It is found that proline residues tend to cause larger kink angles in helical bends, while this effect is not observed in helical disruptions. A further analysis of these kinked helices suggests that a kinked helix usually has 1-2 broken backbone hydrogen bonds with the corresponding N-O distance in the range of 4.2-8.7 Å, whose distribution is sharply peaked at 4.9 Å followed by an exponential decay with increasing distance. Our main aims of this study are to understand the formation of helical kinks and to predict their structural features. Therefore we further performed molecular dynamics (MD) simulations under four simulation scenarios to investigate kink formation in 37 kinked TM helices and 5 unkinked TM helices. The representative models of these kinked helices are predicted by a clustering algorithm, SPICKER, from numerous decoy structures possessing the above generic features of kinked helices. Our results show an accuracy of 95 % in predicting the kink position of kinked TM helices and an error less than 10° in the angle prediction of 71.4 % kinked helices. For unkinked helices, based on various structure similarity tests, our predicted models are highly consistent with their crystal structure. These results provide strong supports for the validity of our method in predicting the structure of TM helices.

Comparative study of plant responses to carbon-based nanomaterials with different morphologies

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

Lahiani, Mohamed H.; Dervishi, Enkeleda; Ivanov, Ilia

The relationship between the morphology of carbon-based nanomaterials (CBNs) and the specific response of plants exposed to CBNs has not been studied systematically. Here, we prove that CBNs with different morphologies can activate cell growth, germination, and plant growth. A tobacco cell culture growth was found to increase by 22%–46% when CBNs such as helical multi-wall carbon nanotubes (MWCNTs), few-layered graphene, long MWCNTs, and short MWCNTs were added to the growth medium at a concentration of 50 μg ml –1. The germination of exposed tomato seeds, as well as the growth of exposed tomato seedlings, were significantly enhanced by themore » addition of all tested CBNs. The presence of CBNs inside exposed seeds was confirmed by transmission electron microscopy and Raman spectroscopy. The effects of helical MWCNTs on gene expression in tomato seeds and seedlings were investigated by microarray technology and real time-PCR. Helical MWCNTs affected a number of genes involved in cellular and metabolic processes and response to stress factors. It was shown that the expression of the tomato water channel gene in tomato seeds exposed to helical MWCNTs was upregulated. Furthermore, these established findings demonstrate that CBNs with different morphologies can cause the same biological effects and share similar mechanisms in planta.« less

Comparative study of plant responses to carbon-based nanomaterials with different morphologies

DOE PAGES

Lahiani, Mohamed H.; Dervishi, Enkeleda; Ivanov, Ilia; ...

2016-05-19

The relationship between the morphology of carbon-based nanomaterials (CBNs) and the specific response of plants exposed to CBNs has not been studied systematically. Here, we prove that CBNs with different morphologies can activate cell growth, germination, and plant growth. A tobacco cell culture growth was found to increase by 22%–46% when CBNs such as helical multi-wall carbon nanotubes (MWCNTs), few-layered graphene, long MWCNTs, and short MWCNTs were added to the growth medium at a concentration of 50 μg ml –1. The germination of exposed tomato seeds, as well as the growth of exposed tomato seedlings, were significantly enhanced by themore » addition of all tested CBNs. The presence of CBNs inside exposed seeds was confirmed by transmission electron microscopy and Raman spectroscopy. The effects of helical MWCNTs on gene expression in tomato seeds and seedlings were investigated by microarray technology and real time-PCR. Helical MWCNTs affected a number of genes involved in cellular and metabolic processes and response to stress factors. It was shown that the expression of the tomato water channel gene in tomato seeds exposed to helical MWCNTs was upregulated. Furthermore, these established findings demonstrate that CBNs with different morphologies can cause the same biological effects and share similar mechanisms in planta.« less

Comparative study of plant responses to carbon-based nanomaterials with different morphologies

NASA Astrophysics Data System (ADS)

Lahiani, Mohamed H.; Dervishi, Enkeleda; Ivanov, Ilia; Chen, Jihua; Khodakovskaya, Mariya

2016-07-01

The relationship between the morphology of carbon-based nanomaterials (CBNs) and the specific response of plants exposed to CBNs has not been studied systematically. Here, we prove that CBNs with different morphologies can activate cell growth, germination, and plant growth. A tobacco cell culture growth was found to increase by 22%-46% when CBNs such as helical multi-wall carbon nanotubes (MWCNTs), few-layered graphene, long MWCNTs, and short MWCNTs were added to the growth medium at a concentration of 50 μg ml-1. The germination of exposed tomato seeds, as well as the growth of exposed tomato seedlings, were significantly enhanced by the addition of all tested CBNs. The presence of CBNs inside exposed seeds was confirmed by transmission electron microscopy and Raman spectroscopy. The effects of helical MWCNTs on gene expression in tomato seeds and seedlings were investigated by microarray technology and real time-PCR. Helical MWCNTs affected a number of genes involved in cellular and metabolic processes and response to stress factors. It was shown that the expression of the tomato water channel gene in tomato seeds exposed to helical MWCNTs was upregulated. These established findings demonstrate that CBNs with different morphologies can cause the same biological effects and share similar mechanisms in planta.

Studying the Transfer of Magnetic Helicity in Solar Active Regions with the Connectivity-based Helicity Flux Density Method

NASA Astrophysics Data System (ADS)

Dalmasse, K.; Pariat, É.; Valori, G.; Jing, J.; Démoulin, P.

2018-01-01

In the solar corona, magnetic helicity slowly and continuously accumulates in response to plasma flows tangential to the photosphere and magnetic flux emergence through it. Analyzing this transfer of magnetic helicity is key for identifying its role in the dynamics of active regions (ARs). The connectivity-based helicity flux density method was recently developed for studying the 2D and 3D transfer of magnetic helicity in ARs. The method takes into account the 3D nature of magnetic helicity by explicitly using knowledge of the magnetic field connectivity, which allows it to faithfully track the photospheric flux of magnetic helicity. Because the magnetic field is not measured in the solar corona, modeled 3D solutions obtained from force-free magnetic field extrapolations must be used to derive the magnetic connectivity. Different extrapolation methods can lead to markedly different 3D magnetic field connectivities, thus questioning the reliability of the connectivity-based approach in observational applications. We address these concerns by applying this method to the isolated and internally complex AR 11158 with different magnetic field extrapolation models. We show that the connectivity-based calculations are robust to different extrapolation methods, in particular with regard to identifying regions of opposite magnetic helicity flux. We conclude that the connectivity-based approach can be reliably used in observational analyses and is a promising tool for studying the transfer of magnetic helicity in ARs and relating it to their flaring activity.

Helical vortices: Quasiequilibrium states and their time evolution

NASA Astrophysics Data System (ADS)

Selçuk, Can; Delbende, Ivan; Rossi, Maurice

2017-08-01

The time evolution of a viscous helical vortex is investigated by direct numerical simulations of the Navier-Stokes equations where helical symmetry is enforced. Using conservation laws in the framework of helical symmetry, we elaborate an initial condition consisting in a finite core vortex, the time evolution of which leads to a generic quasiequilibrium state independent of the initial core size. Numerical results at different helical pitch values provide an accurate characterization in time for such helical states, for which specific techniques have been introduced: helix radius, angular velocity, stream function-velocity-vorticity relationships, and core properties (size, self-similarity, and ellipticity). Viscosity is shown to be at the origin of a small helical velocity component, which we relate to the helical vorticity component. Finally, changes in time of the flow topology are studied using the helical stream function and three-dimensional Lagrangian orbits.

Effect of the magnetic field on the supramolecular structure of chiral smectic C phases: (2)H NMR studies.

PubMed

Domenici, Valentina; Marini, Alberto; Veracini, Carlo Alberto; Zhang, Jing; Dong, Ronald Y

2007-12-21

We present a theoretical and experimental (2)H NMR study of the effect of external magnetic fields on the supramolecular organization of chiral smectic liquid-crystalline mesophases, such as SmC* and re-entrant SmC*. Three experimental cases in which the supramolecular helical structure of the smectic C* phase is unwound by a magnetic field (H), parallel to the helical axes of this phase, are discussed in detail. Unwinding of the helical structure is described by using a theoretical model based on the Landau-de Gennes theory, which allows us to explain the transition temperatures among the SmA, SmC*, and uSmC* phases. The energy-density behavior in the vicinity of the transitions and the value of the critical magnetic field H(C) for unwinding the helical structure are discussed by applying this model to three ferroelectric smectogens (MBHB, 11EB1M7, ZLL7/*), which are studied by (2)H NMR spectroscopy at different magnetic fields (from 2.4 to 9.4 Tesla). Furthermore, the tilt angle of the three smectogens in the SmC* phase has been directly evaluated, for the first time, by comparing the quadrupolar splittings at different magnetic fields. In one case, (2)H NMR angular measurements are used to obtain the tilt angle in the re-entrant smectic C phase.

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.

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.

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.

Investigation of Fully Three-Dimensional Helical RF Field Effects on TWT Beam/Circuit Interaction

NASA Technical Reports Server (NTRS)

Kory, Carol L.

2000-01-01

A fully three-dimensional (3D), time-dependent, helical traveling wave-tube (TWT) interaction model has been developed using the electromagnetic particle-in-cell (PIC) code MAFIA. The model includes a short section of helical slow-wave circuit with excitation fed by RF input/output couplers, and electron beam contained by periodic permanent magnet (PPM) focusing. All components of the model are simulated in three dimensions allowing the effects of the fully 3D helical fields on RF circuit/beam interaction to be investigated for the first time. The development of the interaction model is presented, and predicted TWT performance using 2.5D and 3D models is compared to investigate the effect of conventional approximations used in TWT analyses.

Conformational study of melectin and antapin antimicrobial peptides in model membrane environments

NASA Astrophysics Data System (ADS)

Kocourková, Lucie; Novotná, Pavlína; Čujová, Sabína; Čeřovský, Václav; Urbanová, Marie; Setnička, Vladimír

2017-01-01

Antimicrobial peptides have long been considered as promising compounds against drug-resistant pathogens. In this work, we studied the secondary structure of antimicrobial peptides melectin and antapin using electronic (ECD) and vibrational circular dichroism (VCD) spectroscopies that are sensitive to peptide secondary structures. The results from quantitative ECD spectral evaluation by Dichroweb and CDNN program and from the qualitative evaluation of the VCD spectra were compared. The antimicrobial activity of the selected peptides depends on their ability to adopt an amphipathic α-helical conformation on the surface of the bacterial membrane. Hence, solutions of different zwitterionic and negatively charged liposomes and micelles were used to mimic the eukaryotic and bacterial biological membranes. The results show a significant content of α-helical conformation in the solutions of negatively charged liposomes mimicking the bacterial membrane, thus correlating with the antimicrobial activity of the studied peptides. On the other hand in the solutions of zwitterionic liposomes used as models of the eukaryotic membranes, the fraction of α-helical conformation was lower, which corresponds with their moderate hemolytic activity.

Operational Influence on Thermal Behavior of High-Speed Helical Gear Trains

NASA Technical Reports Server (NTRS)

Handschuh, Robert F.; Kilmain, Charles J.

2006-01-01

An experimental effort has been conducted on an aerospace-quality helical gear train to investigate the thermal behavior of the gear system as many important operational conditions were varied. Drive system performance measurements were made at varying speeds and loads (to 5,000 hp and 15,000 rpm). Also, an analytical effort was undertaken for comparison to the measured results. The influence of the various loss mechanisms from the analysis for this high speed helical gear train gearbox will be presented and compared to the experimental results.

A reconstruction algorithm for helical CT imaging on PI-planes.

PubMed

Liang, Hongzhu; Zhang, Cishen; Yan, Ming

2006-01-01

In this paper, a Feldkamp type approximate reconstruction algorithm is presented for helical cone-beam Computed Tomography. To effectively suppress artifacts due to large cone angle scanning, it is proposed to reconstruct the object point-wisely on unique customized tilted PI-planes which are close to the data collecting helices of the corresponding points. Such a reconstruction scheme can considerably suppress the artifacts in the cone-angle scanning. Computer simulations show that the proposed algorithm can provide improved imaging performance compared with the existing approximate cone-beam reconstruction algorithms.

Comparison of Radiation Dose and Image Quality of Triple-Rule-Out Computed Tomography Angiography Between Conventional Helical Scanning and a Strategy Incorporating Sequential Scanning

PubMed Central

Manheimer, Eric D.; Peters, M. Robert; Wolff, Steven D.; Qureshi, Mehreen A.; Atluri, Prashanth; Pearson, Gregory D.N.; Einstein, Andrew J.

2011-01-01

Triple-rule-out computed tomography angiography (TRO CTA), performed to evaluate the coronary arteries, pulmonary arteries, and thoracic aorta, has been associated with high radiation exposure. Utilization of sequential scanning for coronary computed tomography angiography (CCTA) reduces radiation dose. The application of sequential scanning to TRO CTA is much less well defined. We analyzed radiation dose and image quality from TRO CTA performed in a single outpatient center, comparing scans from a period during which helical scanning with electrocardiographically controlled tube current modulation was used for all patients (n=35) and after adoption of a strategy incorporating sequential scanning whenever appropriate (n=35). Sequential scanning was able to be employed in 86% of cases. The sequential-if-appropriate strategy, compared to the helical-only strategy, was associated with a 61.6% dose decrease (mean dose-length product [DLP] of 439 mGy×cm vs 1144 mGy×cm and mean effective dose of 7.5 mSv vs 19.4 mSv, respectively, p<0.0001). Similarly, there was a 71.5% dose reduction among 30 patients scanned with the sequential protocol compared to 40 patients scanned with the helical protocol under either strategy (326 mGy×cm vs 1141 mGy×cm and 5.5 mSv vs 19.4 mSv, respectively, p<0.0001). Although image quality did not differ between strategies, there was a non-statistically significant trend towards better quality in the sequential protocol compared to the helical protocol. In conclusion, approaching TRO CTA with a diagnostic strategy of sequential scanning as appropriate offers a marked reduction in radiation dose while maintaining image quality. PMID:21306693

Transferability of different classical force fields for right and left handed α-helices constructed from enantiomeric amino acids.

PubMed

Biswas, Santu; Sarkar, Sujit; Pandey, Prithvi Raj; Roy, Sudip

2016-02-21

Amino acids can form d and l enantiomers, of which the l enantiomer is abundant in nature. The naturally occurring l enantiomer has a greater preference for a right handed helical conformation, and the d enantiomer for a left handed helical conformation. The other conformations, that is, left handed helical conformations of the l enantiomers and right handed helical conformations of the d enantiomers, are not common. The energetic differences between left and right handed alpha helical peptide chains constructed from enantiomeric amino acids are investigated using quantum chemical calculations (using the M06/6-311g(d,p) level of theory). Further, the performances of commonly used biomolecular force fields (OPLS/AA, CHARMM27/CMAP and AMBER) to represent the different helical conformations (left and right handed) constructed from enantiomeric (D and L) amino acids are evaluated. 5- and 10-mer chains from d and l enantiomers of alanine, leucine, lysine, and glutamic acid, in right and left handed helical conformations, are considered in the study. Thus, in total, 32 α-helical polypeptides (4 amino acids × 4 conformations of 5-mer and 10-mer) are studied. Conclusions, with regards to the performance of the force fields, are derived keeping the quantum optimized geometry as the benchmark, and on the basis of phi and psi angle calculations, hydrogen bond analysis, and different long range helical order parameters.

Fluid-Dynamic Optimal Design of Helical Vascular Graft for Stenotic Disturbed Flow

PubMed Central

Ha, Hojin; Hwang, Dongha; Choi, Woo-Rak; Baek, Jehyun; Lee, Sang Joon

2014-01-01

Although a helical configuration of a prosthetic vascular graft appears to be clinically beneficial in suppressing thrombosis and intimal hyperplasia, an optimization of a helical design has yet to be achieved because of the lack of a detailed understanding on hemodynamic features in helical grafts and their fluid dynamic influences. In the present study, the swirling flow in a helical graft was hypothesized to have beneficial influences on a disturbed flow structure such as stenotic flow. The characteristics of swirling flows generated by helical tubes with various helical pitches and curvatures were investigated to prove the hypothesis. The fluid dynamic influences of these helical tubes on stenotic flow were quantitatively analysed by using a particle image velocimetry technique. Results showed that the swirling intensity and helicity of the swirling flow have a linear relation with a modified Germano number (Gn*) of the helical pipe. In addition, the swirling flow generated a beneficial flow structure at the stenosis by reducing the size of the recirculation flow under steady and pulsatile flow conditions. Therefore, the beneficial effects of a helical graft on the flow field can be estimated by using the magnitude of Gn*. Finally, an optimized helical design with a maximum Gn* was suggested for the future design of a vascular graft. PMID:25360705

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

Miloshevich, George; Lingam, Manasvi; Morrison, Philip J.

Recent progress regarding the noncanonical Hamiltonian formulation of extended magnetohydrodynamics (XMHD), a model with Hall drift and electron inertia, is summarized. The advantages of the Hamiltonian approach are invoked to study some general properties of XMHD turbulence, and to compare them against their ideal MHD counterparts. For instance, the helicity flux transfer rates for XMHD are computed, and Liouville's theorem for this model is also verified. The latter is used, in conjunction with the absolute equilibrium states, to arrive at the spectra for the invariants, and to determine the direction of the cascades, e.g., generalizations of the well-known ideal MHDmore » inverse cascade of magnetic helicity. After a similar analysis is conducted for XMHD by inspecting second order structure functions and absolute equilibrium states, a couple of interesting results emerge. When cross helicity is taken to be ignorable, the inverse cascade of injected magnetic helicity also occurs in the Hall MHD range-this is shown to be consistent with previous results in the literature. In contrast, in the inertial MHD range, viz at scales smaller than the electron skin depth, all spectral quantities are expected to undergo direct cascading. Finally, the consequences and relevance of our results in space and astrophysical plasmas are also briefly discussed.« less

Analysis of inter-residue contacts reveals folding stabilizers in P-loops of potassium, sodium, and TRPV channels.

PubMed

Korkosh, V S; Zhorov, B S; Tikhonov, D B

2016-05-01

The family of P-loop channels includes potassium, sodium, calcium, cyclic nucleotide-gated and TRPV channels, as well as ionotropic glutamate receptors. Despite vastly different physiological and pharmacological properties, the channels have structurally conserved folding of the pore domain. Furthermore, crystallographic data demonstrate surprisingly similar mutual disposition of transmembrane and membrane-diving helices. To understand determinants of this conservation, here we have compared available high-resolution structures of sodium, potassium, and TRPV1 channels. We found that some residues, which are in matching positions of the sequence alignment, occur in different positions in the 3D alignment. Surprisingly, we found 3D mismatches in well-packed P-helices. Analysis of energetics of individual residues in Monte Carlo minimized structures revealed cyclic patterns of energetically favorable inter- and intra-subunit contacts of P-helices with S6 helices. The inter-subunit contacts are rather conserved in all the channels, whereas the intra-subunit contacts are specific for particular types of the channels. Our results suggest that these residue-residue contacts contribute to the folding stabilization. Analysis of such contacts is important for structural and phylogenetic studies of homologous proteins.

Helical CT scan with 2D and 3D reconstructions and virtual endoscopy versus conventional endoscopy in the assessment of airway disease in neonates, infants and children.

PubMed

Yunus, Mahira

2012-11-01

To study the use of helical computed tomography 2-D and 3-D images, and virtual endoscopy in the evaluation of airway disease in neonates, infants and children and its value in lesion detection, characterisation and extension. Conducted at Al-Noor Hospital, Makkah, Saudi Arabia, from January 1 to June 30, 2006, the study comprised of 40 patients with strider, having various causes of airway obstruction. They were examined by helical CT scan with 2-D and 3-D reconstructions and virtual endoscopy. The level and characterisation of lesions were carried out and results were compared with actual endoscopic findings. Conventional endoscopy was chosen as the gold standard, and the evaluation of endoscopy was done in terms of sensitivity and specificity of the procedure. For statistical purposes, SPSS version 10 was used. All CT methods detected airway stenosis or obstruction. Accuracy was 98% (n=40) for virtual endoscopy, 96% (n=48) for 3-D external rendering, 90% (n=45) for multiplanar reconstructions and 86% (n=43) for axial images. Comparing the results of 3-D internal and external volume rendering images with conventional endoscopy for detection and grading of stenosis were closer than with 2-D minimum intensity multiplanar reconstruction and axial CT slices. Even high-grade stenosis could be evaluated with virtual endoscope through which conventional endoscope cannot be passed. A case of 4-year-old patient with tracheomalacia could not be diagnosed by helical CT scan and virtual bronchoscopy which was diagriosed on conventional endoscopy and needed CT scan in inspiration and expiration. Virtual endoscopy [VE] enabled better assessment of stenosis compared to the reading of 3-D external rendering, 2-D multiplanar reconstruction [MPR] or axial slices. It can replace conventional endoscopy in the assessment of airway disease without any additional risk.

Comparison of tip apex distance and cut-out complications between helical blades and lag screws in intertrochanteric fractures among the elderly: a meta-analysis.

PubMed

Li, Shuang; Chang, Shi-Min; Niu, Wen-Xin; Ma, Hui

2015-11-01

To investigate whether helical blade implant systems have advantages in terms of tip apex distance (TAD) and cut-out rate in comparison to conventional lag screws for intertrochanteric fractures in a geriatric population. Methods: Relevant articles were sourced from the MEDLINE, Embase, Ovid and Cochrane Library databases from inception through March 2015. All randomized controlled trials (RCTs) comparing outcomes between helical blade and lag screw implant systems were selected. Mean TAD values and reported cut-out complications were noted. Each author independently assessed the relevance of the enrolled studies and the quality of the extracted data. Data were analyzed using R software. Ten studies including 1831 patients were eligible for this review, seven of which were included in a combined analysis of dichotomous outcomes and five in a combined analysis of continuous outcomes. The results revealed that, compared with lag screw implantations, the use of helical blades led to a lower rate of cut-out complications (95 % CI: 0.28–0.96, P = 0.036). Patients who experienced cut-out complications had a significantly greater tip apex distance (95 % CI: 0.68–1.34, P < 0.001). However, the actual tip apex distances were similar between the screw group and blade group (95 % CI: −0.44–0.79, P = 0.58). No difference in TAD values was found between blades and screws. In addition, the cut-out risk in the blade-design group was lower than that of the screw group. Therefore, TAD is not an accurate predictor of cut-out risk.

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.

Improving the output voltage waveform of an intense electron-beam accelerator based on helical type Blumlein pulse forming line

NASA Astrophysics Data System (ADS)

Cheng, Xin-Bing; Liu, Jin-Liang; Zhang, Hong-Bo; Feng, Jia-Huai; Qian, Bao-Liang

2010-07-01

The Blumlein pulse forming line (BPFL) consisting of an inner coaxial pulse forming line (PFL) and an outer coaxial PFL is widely used in the field of pulsed power, especially for intense electron-beam accelerators (IEBA). The output voltage waveform determines the quality and characteristics of the output beam current of the IEBA. Comparing with the conventional BPFL, an IEBA based on a helical type BPFL can increase the duration of the output voltage in the same geometrical volume. However, for the helical type BPFL, the voltage waveform on a matched load may be distorted which influences the electron-beam quality. In this paper, an IEBA based on helical type BPFL is studied theoretically. Based on telegrapher equations of the BPFL, a formula for the output voltage of IEBA is obtained when the transition section is taken into account, where the transition section is between the middle cylinder of BPFL and the load. From the theoretical analysis, it is found that the wave impedance and transit time of the transition section influence considerably the main pulse voltage waveform at the load, a step is formed in front of the main pulse, and a sharp spike is also formed at the end of the main pulse. In order to get a well-shaped square waveform at the load and to improve the electron-beam quality of such an accelerator, the wave impedance of the transition section should be equal to that of the inner PFL of helical type BPFL and the transit time of the transition section should be designed as short as possible. Experiments performed on an IEBA with the helical type BPFL show reasonable agreement with theoretical analysis.

Collagenolytic Matrix Metalloproteinase Activities toward Peptomeric Triple-Helical Substrates.

PubMed

Stawikowski, Maciej J; Stawikowska, Roma; Fields, Gregg B

2015-05-19

Although collagenolytic matrix metalloproteinases (MMPs) possess common domain organizations, there are subtle differences in their processing of collagenous triple-helical substrates. In this study, we have incorporated peptoid residues into collagen model triple-helical peptides and examined MMP activities toward these peptomeric chimeras. Several different peptoid residues were incorporated into triple-helical substrates at subsites P3, P1, P1', and P10' individually or in combination, and the effects of the peptoid residues were evaluated on the activities of full-length MMP-1, MMP-8, MMP-13, and MMP-14/MT1-MMP. Most peptomers showed little discrimination between MMPs. However, a peptomer containing N-methyl Gly (sarcosine) in the P1' subsite and N-isobutyl Gly (NLeu) in the P10' subsite was hydrolyzed efficiently only by MMP-13 [nomenclature relative to the α1(I)772-786 sequence]. Cleavage site analysis showed hydrolysis at the Gly-Gln bond, indicating a shifted binding of the triple helix compared to the parent sequence. Favorable hydrolysis by MMP-13 was not due to sequence specificity or instability of the substrate triple helix but rather was based on the specific interactions of the P7' peptoid residue with the MMP-13 hemopexin-like domain. A fluorescence resonance energy transfer triple-helical peptomer was constructed and found to be readily processed by MMP-13, not cleaved by MMP-1 and MMP-8, and weakly hydrolyzed by MT1-MMP. The influence of the triple-helical structure containing peptoid residues on the interaction between MMP subsites and individual substrate residues may provide additional information about the mechanism of collagenolysis, the understanding of collagen specificity, and the design of selective MMP probes.

Decay of helical and nonhelical magnetic knots

NASA Astrophysics Data System (ADS)

Candelaresi, Simon; Brandenburg, Axel

2011-07-01

We present calculations of the relaxation of magnetic field structures that have the shape of particular knots and links. A set of helical magnetic flux configurations is considered, which we call n-foil knots of which the trefoil knot is the most primitive member. We also consider two nonhelical knots; namely, the Borromean rings as well as a single interlocked flux rope that also serves as the logo of the Inter-University Centre for Astronomy and Astrophysics in Pune, India. The field decay characteristics of both configurations is investigated and compared with previous calculations of helical and nonhelical triple-ring configurations. Unlike earlier nonhelical configurations, the present ones cannot trivially be reduced via flux annihilation to a single ring. For the n-foil knots the decay is described by power laws that range form t-2/3 to t-1/3, which can be as slow as the t-1/3 behavior for helical triple-ring structures that were seen in earlier work. The two nonhelical configurations decay like t-1, which is somewhat slower than the previously obtained t-3/2 behavior in the decay of interlocked rings with zero magnetic helicity. We attribute the difference to the creation of local structures that contain magnetic helicity which inhibits the field decay due to the existence of a lower bound imposed by the realizability condition. We show that net magnetic helicity can be produced resistively as a result of a slight imbalance between mutually canceling helical pieces as they are being driven apart. We speculate that higher order topological invariants beyond magnetic helicity may also be responsible for slowing down the decay of the two more complicated nonhelical structures mentioned above.

Magnetic helicity in emerging solar active regions

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

Liu, Y.; Hoeksema, J. T.; Bobra, M.

Using vector magnetic field data from the Helioseismic and Magnetic Imager instrument aboard the Solar Dynamics Observatory, we study magnetic helicity injection into the corona in emerging active regions (ARs) and examine the hemispheric helicity rule. In every region studied, photospheric shearing motion contributes most of the helicity accumulated in the corona. In a sample of 28 emerging ARs, 17 follow the hemisphere rule (61% ± 18% at a 95% confidence interval). Magnetic helicity and twist in 25 ARs (89% ± 11%) have the same sign. The maximum magnetic twist, which depends on the size of an AR, is inferredmore » in a sample of 23 emerging ARs with a bipolar magnetic field configuration.« less

Role of helicity in triad interactions in three-dimensional turbulence investigated by a new shell model

NASA Astrophysics Data System (ADS)

Rathmann, Nicholas M.; Ditlevsen, Peter D.

2016-09-01

Fully developed homogeneous isotropic turbulence in two dimensions is fundamentally different from that in three dimensions. In two dimensions, the simultaneous inviscid conservation of both kinetic energy and enstrophy within the inertial range of scales leads to a forward cascade of enstrophy and a reverse cascade of energy. In three dimensions, helicity, the integral of the scalar product of velocity and vorticity, is also an inviscid flow invariant along with the energy. Unlike the enstrophy, however, the helicity does not block the forward cascade of energy to small scales. Energy and helicity are conserved not only globally but also within each nonlinear triadic interaction between three plane waves in the spectral form of the Navier-Stokes equation (NSE). By decomposing each plane wave into two helical modes of opposite helicities, each triadic interaction is split into a set of eight helical triadic interactions between helical modes [F. Waleffe, Phys. Fluids A 4, 350 (1992), 10.1063/1.858309]. Recently it was found that a subset of these helical interactions, which render both signs of helicity separately conserved (enstrophy-like), leads to an inverse cascade of (part of) the energy [L. Biferale et al., Phys. Rev. Lett. 108, 164501 (2012), 10.1103/PhysRevLett.108.164501]. Motivated by this finding we introduce a new shell model, obtained from the NSE expressed in the helical basis, allowing the eight helical interactions to be coupled as in the NSE and their relative contributions evaluated as a function of both the net helicity input and triad geometry. By numerically integrating the new model, we find that the intermittency of the energy cascade decreases with the net helicity input. Studying the partitioning of the energy cascade between the eight helical interactions, we find that the decrease in intermittency is related to a shift in the dominating helical interactions when helically forced, two of which exhibit a larger cascade intermittency than the other six interactions. Among the relatively local triad geometries considered here, the partitioning of the energy and helicity cascades between the eight helical interactions shows no sign of change with triad geometry.

Computation of Relative Magnetic Helicity in Spherical Coordinates

NASA Astrophysics Data System (ADS)

Moraitis, Kostas; Pariat, Étienne; Savcheva, Antonia; Valori, Gherardo

2018-06-01

Magnetic helicity is a quantity of great importance in solar studies because it is conserved in ideal magnetohydrodynamics. While many methods for computing magnetic helicity in Cartesian finite volumes exist, in spherical coordinates, the natural coordinate system for solar applications, helicity is only treated approximately. We present here a method for properly computing the relative magnetic helicity in spherical geometry. The volumes considered are finite, of shell or wedge shape, and the three-dimensional magnetic field is considered to be fully known throughout the studied domain. Testing of the method with well-known, semi-analytic, force-free magnetic-field models reveals that it has excellent accuracy. Further application to a set of nonlinear force-free reconstructions of the magnetic field of solar active regions and comparison with an approximate method used in the past indicates that the proposed method can be significantly more accurate, thus making our method a promising tool in helicity studies that employ spherical geometry. Additionally, we determine and discuss the applicability range of the approximate method.

FtsZ rings and helices: physical mechanisms for the dynamic alignment of biopolymers in rod-shaped bacteria.

PubMed

Fischer-Friedrich, Elisabeth; Friedrich, Benjamin M; Gov, Nir S

2012-02-01

In many bacterial species, the protein FtsZ forms a cytoskeletal ring that marks the future division site and scaffolds the division machinery. In rod-shaped bacteria, most frequently membrane-attached FtsZ rings or ring fragments are reported and occasionally helices. By contrast, axial FtsZ clusters have never been reported. In this paper, we investigate theoretically how dynamic FtsZ aggregates align in rod-shaped bacteria. We study systematically different physical mechanisms that affect the alignment of FtsZ polymers using a computational model that relies on autocatalytic aggregation of FtsZ filaments at the membrane. Our study identifies a general tool kit of physical and geometrical mechanisms by which rod-shaped cells align biopolymer aggregates. Our analysis compares the relative impact of each mechanism on the circumferential alignment of FtsZ as observed in rod-shaped bacteria. We determine spontaneous curvature of FtsZ polymers and axial confinement of FtsZ on the membrane as the strongest factors. Including Min oscillations in our model, we find that these stabilize axial and helical clusters on short time scales, but promote the formation of an FtsZ ring at the cell middle at longer times. This effect could provide an explanation to the long standing puzzle of transiently observed oscillating FtsZ helices in Escherichia coli cells prior to cell division.

Gyrosynchrotron radiation formulae. [analysis of electron moving along a helical path in a magnetoactive medium

NASA Technical Reports Server (NTRS)

Ko, H. C.

1973-01-01

The wave-normal emissivity and the ray emissivity formulas for an electron moving along a helical path in a magnetoactive medium are presented. Simplified formulas for the case of an isotropic plasma are also given. Because of the helical motion of the electron, a difference exists between the radiated power per unit solid angle and the received power per unit solid angle. The relation between these two quantities in a magnetoactive medium is shown. Results are compared with those obtained by others, and the sources of discrepancies are pointed out.

N-terminal segments modulate the α-helical propensities of the intrinsically disordered basic regions of bZIP proteins.

PubMed

Das, Rahul K; Crick, Scott L; Pappu, Rohit V

2012-02-17

Basic region leucine zippers (bZIPs) are modular transcription factors that play key roles in eukaryotic gene regulation. The basic regions of bZIPs (bZIP-bRs) are necessary and sufficient for DNA binding and specificity. Bioinformatic predictions and spectroscopic studies suggest that unbound monomeric bZIP-bRs are uniformly disordered as isolated domains. Here, we test this assumption through a comparative characterization of conformational ensembles for 15 different bZIP-bRs using a combination of atomistic simulations and circular dichroism measurements. We find that bZIP-bRs have quantifiable preferences for α-helical conformations in their unbound monomeric forms. This helicity varies from one bZIP-bR to another despite a significant sequence similarity of the DNA binding motifs (DBMs). Our analysis reveals that intramolecular interactions between DBMs and eight-residue segments directly N-terminal to DBMs are the primary modulators of bZIP-bR helicities. We test the accuracy of this inference by designing chimeras of bZIP-bRs to have either increased or decreased overall helicities. Our results yield quantitative insights regarding the relationship between sequence and the degree of intrinsic disorder within bZIP-bRs, and might have general implications for other intrinsically disordered proteins. Understanding how natural sequence variations lead to modulation of disorder is likely to be important for understanding the evolution of specificity in molecular recognition through intrinsically disordered regions (IDRs). Copyright © 2011 Elsevier Ltd. All rights reserved.

Propulsion of helical flagella near boundaries

NASA Astrophysics Data System (ADS)

Rodenborn, Bruce; Giesbrecht, Grant; Ni, Katha; Vock, Isaac

The presence of nearby boundaries is known to have dramatic effects on the swimming behavior of microorganisms because of the no-slip condition at the boundary. Microorganisms that use a helical flagellum experience forces both along the axis of the helix and in the direction perpendicular to the axis. These low Reynolds number boundary effects have primarily been studied using live bacteria and using numerical simulations. However, small scale measurements give limited information about the forces and torques on the microorganisms. Furthermore, numerical studies are approximate because they have generally used Stokeslet-based simulations with image Stokeslets to represent the effects of the boundaries. Instead, we directly measure the propulsion of macroscopic helical flagella with diameter 12 mm using a fluid with viscosity 105 times that of water to ensure the Reynolds number in the experiments is much less than unity, just as for bacteria. We measure the parallel and perpendicular forces as a function of boundary distance to determine the nonzero elements of the propulsive matrix for axial rotation near a boundary. We then compare our results to the theory and simulations of Lauga et al. and to biological measurements.

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.

Alternating phenylene and furan/pyrrole/thiophene units-based oligomers: A computational study of the structures and optoelectronic properties

NASA Astrophysics Data System (ADS)

Sahu, Harikrishna; Shukla, Rishabh; Goswami, Juri; Gaur, Priyank; Panda, Aditya N.

2018-01-01

Structural and optoelectronic properties of phenylene-furan, phenylene-pyrrole and phenylene-thiophene oligomers are reported using density functional theory methods. Studies reveal that stabilities of conformers change with increasing chain length, and helical conformers are energetically feasible for large oligomers of the studied systems, due to stacking interactions between adjacent helical turns. Absorption spectra of helices are dominated by multiple number of electronic transitions other than the S0 →S1 , involving orbitals other than the HOMO/LUMO. All studied helices are optically active having similar pattern of negative and positive peaks in the CD spectra.

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

PubMed

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

2007-01-01

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

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.

Iron(II) supramolecular helicates interfere with the HIV-1 Tat-TAR RNA interaction critical for viral replication.

PubMed

Malina, Jaroslav; Hannon, Michael J; Brabec, Viktor

2016-07-12

The interaction between the HIV-1 transactivator protein Tat and TAR (transactivation responsive region) RNA, plays a critical role in HIV-1 transcription. Iron(II) supramolecular helicates were evaluated for their in vitro activity to inhibit Tat-TAR RNA interaction using UV melting studies, electrophoretic mobility shift assay, and RNase A footprinting. The results demonstrate that iron(II) supramolecular helicates inhibit Tat-TAR interaction at nanomolar concentrations by binding to TAR RNA. These studies provide a new insight into the biological potential of metallosupramolecular helicates.

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

PubMed

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

2014-08-12

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

Interaction of anesthetic molecules with α-helix and polyproline II extended helix of long-chain poly-L-lysine

NASA Astrophysics Data System (ADS)

Cieślik-Boczula, Katarzyna; Rospenk, Maria

2018-01-01

The effect of halothane, enflurane, sevoflurane, and isoflurane molecules, as volatile anesthetics, on the α-helices and polyproline II extended helices (PPII) of long-chain poly-L-lysine (PLL) were studied using Fourier-transform infrared and vibrational circular dichroism spectroscopy. Uncharged and charged α-helices, as well as charged extended PPII helices, were subjected to anesthetic actions in solvents with different pD values or methanol to water ratios. A crucial factor responsible for hindering the anesthetic-PLL interactions is shown to be the ionization of amino groups of the PLL side chains. The α-helix to β-sheet transition was triggered only for the uncharged α-helical structures of PLL by the nonpolar anesthetics under study.

Relative stabilities of triple helices composed of combinations of DNA, RNA and 2'-O-methyl-RNA backbones: chimeric circular oligonucleotides as probes.

PubMed

Wang, S; Kool, E T

1995-04-11

Described is a systematic study of the effects of varied backbone structure on the stabilities of pyr.pur.pyr triple helices. The effects were measured using six circular 34 base oligonucleotides containing DNA (D), RNA (R) and/or 2'-O-methyl-RNA (M) residues designed to bind a complementary single-stranded purine target strand by triple helix formation. Eighteen different backbone combinations were studied at pH 5.5 and 7.0 by optical melting experiments and the results compared with the stabilities of the corresponding Watson-Crick duplexes. When the target purine strand is DNA, all circles form pH-dependent triple helical complexes which are considerably stronger than the duplexes alone. When RNA is the target, five of the nine complexes studied are of the pH-dependent triplex type and the other four complexes are not significantly stronger than the corresponding duplexes. The results are useful in the design of the highest affinity ligands for single- and double-stranded DNAs and RNAs and also point out novel ways to engender DNA- or RNA-selective binding.

Topological and statistical properties of nonlinear force-free fields

NASA Astrophysics Data System (ADS)

Mangalam, A.; Prasad, A.

2018-01-01

We use our semi-analytic solution of the nonlinear force-free field equation to construct three-dimensional magnetic fields that are applicable to the solar corona and study their statistical properties for estimating the degree of braiding exhibited by these fields. We present a new formula for calculating the winding number and compare it with the formula for the crossing number. The comparison is shown for a toy model of two helices and for realistic cases of nonlinear force-free fields; conceptually the formulae are nearly the same but the resulting distributions calculated for a given topology can be different. We also calculate linkages, which are useful topological quantities that are independent measures of the contribution of magnetic braiding to the total free energy and relative helicity of the field. Finally, we derive new analytical bounds for the free energy and relative helicity for the field configurations in terms of the linking number. These bounds will be of utility in estimating the braided energy available for nano-flares or for eruptions.

Separation of overlapping vibrational peaks in terahertz spectra using two-dimensional correlation spectroscopy

NASA Astrophysics Data System (ADS)

Hoshina, Hiromichi; Ishii, Shinya; Otani, Chiko

2014-07-01

In this study, the terahertz (THz) absorption spectra of poly(3-hydroxybutyrate) (PHB) were measured during isothermal crystallization at 90-120 °C. The temporal changes in the absorption spectra were analyzed using two-dimensional correlation spectroscopy (2DCOS). In the asynchronous plot, cross peaks were observed around 2.4 THz, suggesting that two vibrational modes overlap in the raw spectrum. By comparing this to the peak at 2.9 THz corresponding to the stretching mode of the helical structure of PHB and the assignment obtained using polarization spectroscopy, we concluded that the high-frequency band could be attributed to the vibration of the helical structure and the low-frequency band to the vibration between the helical structures. The exact frequencies of the overlapping vibrational bands and their assignments provide a new means to inspect the thermal behavior of the intermolecular vibrational modes. The large red-shift of the interhelix vibrational mode suggests a large anharmonicity in the vibrational potential.

Impurity transport in enhanced confinement regimes in RFX-mod Reversed Field Pinch

NASA Astrophysics Data System (ADS)

Carraro, Lorella; Menmuir, Sheena; Fassina, Alessandro

2010-11-01

The results of impurity transport studies in RFX-mod enhanced confinement quasi-single helicity (QSH) and single helical axis (SHAx) regimes are presented and discussed. The impurity diffusion coefficient and pinch velocity are obtained through comparing experimental emission pattern (line emission and SXR time evolutions, SXR profiles) with the results of a 1-D impurity transport code. Previous analysis [S. Menmuir et al. to be published in Plasma Phys. Contr. Fus.] of impurity transport in RFX-mod standard discharges showed that the impurity pinch velocity, always directed outwards, features a barrier with high values around r/a = 0.8, where the diffusion coefficient decreases by one order of magnitude. In the QSH regime, the transition region in D and v is more internal and the barrier in velocity is wider and stronger. New results have been obtained in experiments with Ni laser blow-off (LBO) injection in high current discharges (Ip>1.5 MA) with long lasting QSH, to better characterize the Ni behavior inside the helical magnetic topology.

SU-F-J-117: Impact of Motion Artifacts On Image Quality and Accuracy of Tumor Motion Reconstruction in 4D CT-On-Rails and MV-CBCT Scans: A Phantom Study

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

Lin, T; Ma, C

Purpose: To compare and quantify respiratory motion artifacts in images from free breathing 4D-CT-on-Rails(CTOR) and those from MV-Cone-beam-CT(MVCB) and facilitate respiratory motion guided radiation therapy. Methods: 4D-CTOR: Siemens Somatom CT-on-Rails system with Anzai belt loaded with pressure sensor load cells. 4D scans were performed in helical mode, pitch 0.1, gantry rotation time 0.5s, 1.5mm slice thickness, 120kVp, 400 mAs. Normal and fast breathing (>12rpm) scanning protocols were investigated. Helical scan, AIP(average intensity projection) and MIP(maximum intensity projection) were generated from 4D-CTOR scans with amplitude sorting into 10 phases.MVCB: Siemens Artiste diamond view(1MV)MVCB was performed with 5MU thorax protocol with 60more » second of full rotation.Phantom: Anzai AZ-733V respiratory phantom. The settings were set to normal and resp. modes with repetition rates at 15 rpm and 10 rpm. Surgical clips, acrylic, wooden, rubber and lung density, total six mock-ups were scanned and compared in this study.Signal-to-noise ratio(SNR), contrast-to-noise ratio(CNR) and reconstructed motion volume were compared to different respiratory setups for the mock-ups. Results: Reconstructed motion volume was compared to the real object volume for the six test mock-ups. It shows that free breathing helical in all instances underestimates the object excursions largest to −67.4% and least −6.3%. Under normal breathing settings, MIP can predict very precise motion volume with minimum 0.4% and largest −13.9%. MVCB shows underestimate of the motion volume with −1.11% minimum and −18.0% maximum. With fast breathing, AIP provides bad representation of the object motion; however, the MIP can predict the motion volume with −2.0% to −11.4% underestimate. Conclusion: Respiratory motion guided radiation therapy requires good motion recording. This study shows that regular CTOR helical scans provides bad guidance, 4D CTOR AIP cannot represent the fast breathing pattern, MIP can represent the best motion volume, MVCBCT can only be used for normal breathing with acceptable uncertainties.« less

Students' experiences with a longitudinal skills training program on breaking bad news: A follow-up study.

PubMed

Brouwers, M H; Bor, H; Laan, R; van Weel, C; van Weel-Baumgarten, E

2018-05-07

Breaking bad news (BBN) should be trained, preferably early and following a helical model with multiple sessions over time, including feedback on performance. It's unclear how medical students evaluate such an approach. We gathered student opinions regarding a helical BBN training programme, the feedback and emotional support they received, and the applicability of the skills training immediately after BBN skills training (Q1) and after finishing their clinical clerkships (Q2). Students find a helical curriculum useful, but this declines on follow-up. At Q2 students report less satisfaction with the amount of feedback and emotional support they received and report that the skills training was less applicable in clinical practice compared to what they reported at Q1. A helical BBN training programme with early exposure seems to lead to a shift from students being unconsciously incompetent to consciously incompetent. Students would have appreciated more emotional support and feedback. We recommend more feedback and emotional support after BBN during clerkships. The gap between classroom and practice can be diminished by emphasizing real life role play and clinical role models should demonstrate continuity and agreement between the skills that are taught and those that are used in clinical practice. Copyright © 2018 Elsevier B.V. All rights reserved.

On the structure and statistical theory of turbulence of extended magnetohydrodynamics

DOE PAGES

Miloshevich, George; Lingam, Manasvi; Morrison, Philip J.

2017-01-16

Recent progress regarding the noncanonical Hamiltonian formulation of extended magnetohydrodynamics (XMHD), a model with Hall drift and electron inertia, is summarized. The advantages of the Hamiltonian approach are invoked to study some general properties of XMHD turbulence, and to compare them against their ideal MHD counterparts. For instance, the helicity flux transfer rates for XMHD are computed, and Liouville's theorem for this model is also verified. The latter is used, in conjunction with the absolute equilibrium states, to arrive at the spectra for the invariants, and to determine the direction of the cascades, e.g., generalizations of the well-known ideal MHDmore » inverse cascade of magnetic helicity. After a similar analysis is conducted for XMHD by inspecting second order structure functions and absolute equilibrium states, a couple of interesting results emerge. When cross helicity is taken to be ignorable, the inverse cascade of injected magnetic helicity also occurs in the Hall MHD range-this is shown to be consistent with previous results in the literature. In contrast, in the inertial MHD range, viz at scales smaller than the electron skin depth, all spectral quantities are expected to undergo direct cascading. Finally, the consequences and relevance of our results in space and astrophysical plasmas are also briefly discussed.« less

Maintaining ear aesthetics in helical rim reconstruction.

PubMed

Taylor, James M; Rajan, Ruchika; Dickson, John K; Mahajan, Ajay L

2014-03-01

Wedge resections of the helical rim may result in a significant deformity of the ear with the ear not only smaller but cupped and prominent too. Our technique involves resection of the wedge in the scaphal area without extending into the concha followed by advancement of the helical rim into the defect. This technique is most suitable for peripheral defects of the helical rim, in the middle third. Our modified surgical technique was applied to reconstruction of the pinna after resection of the tumor in 12 patients. Free cartilaginous helical rim, length of helical rim to be resected, and projection of the ear from the mastoid was measured. This was then compared with measurements after the operation, and the patient satisfaction assessed with a visual analog scale. The free cartilaginous rim was 91.67 ± 5.61 mm. Of this, 21.92 ± 3.78 mm was resected, which amounted to 23.84% ± 3.35% of the rim. Although this resulted in a mean increase in ear projection of 6.42 ± 1.68 mm, the aesthetic outcome was good (visual analog scale, 9.08 ± 0.9). This technique reduces cupping and does not make the ear as prominent as it may do after a conventional wedge resection and results in high patient satisfaction.

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

PubMed Central

Nugent, Timothy; Jones, David T.

2010-01-01

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

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.

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

Impact of helical organization on the photovoltaic properties of oligothiophene supramolecular polymers† †Electronic supplementary information (ESI) available: Synthesis and characterization of 3 and 4, UV-vis spectra, solar cell device properties and AFM images. See DOI: 10.1039/c7sc05093c

PubMed Central

Ouchi, Hayato; Kizaki, Takahiro; Yamato, Masaki; Lin, Xu; Hoshi, Nagahiro; Silly, Fabien; Kajitani, Takashi; Fukushima, Takanori

2018-01-01

Helical self-assembly of functional π-conjugated molecules offers unique photochemical and electronic properties in the spectroscopic level, but there are only a few examples that demonstrate their positive impact on the optoelectronic device level. Here, we demonstrate that hydrogen-bonded tapelike supramolecular polymers of a barbiturated oligo(alkylthiophene) show notable improvement in their photovoltaic properties upon organizing into helical nanofibers. A tapelike hydrogen-bonded supramolecular array of barbiturated oligo(butylthiophene) molecules was directly visualized by STM at a liquid–solid interface. TEM, AFM and XRD revealed that the tapelike supramolecular polymers further organize into helical nanofibers in solution and bulk states. Bulk heterojunction solar cells of the helical nanofibers and soluble fullerene showed a power conversion efficiency of 4.5%, which is markedly high compared to that of the regioisomer of butyl chains organizing into 3D lamellar agglomerates. PMID:29780493

Non-lignified helical cell wall thickenings in root cortical cells of Aspleniaceae (Polypodiales): histology and taxonomical significance

PubMed Central

Leroux, O.; Bagniewska-Zadworna, A.; Rambe, S. K.; Knox, J. P.; Marcus, S. E.; Bellefroid, E.; Stubbe, D.; Chabbert, B.; Habrant, A.; Claeys, M.; Viane, R. L. L.

2011-01-01

Background and Aims Extraxylary helical cell wall thickenings in vascular plants are not well documented, except for those in orchid velamen tissues which have been studied extensively. Reports on their occurrence in ferns exist, but detailed information is missing. The aim of this study is to focus on the broad patterns of structure and composition and to study the taxonomic occurrence of helical cell wall thickenings in the fern family Aspleniaceae. Methods Structural and compositional aspects of roots have been examined by means of light, electron, epifluorescence and laser scanning confocal microscopy. To assess the taxonomical distribution of helical cell wall thickenings a molecular phylogenetic analysis based on rbcL sequences of 64 taxa was performed. Key Results The helical cell wall thickenings of all examined species showed considerable uniformity of design. The pattern consists of helical, regularly bifurcating and anastomosing strands. Compositionally, the cell wall thickenings were found to be rich in homogalacturonan, cellulose, mannan and xyloglucan. Thioacidolysis confirmed our negative phloroglucinol staining tests, demonstrating the absence of lignins in the root cortex. All taxa with helical cell wall thickenings formed a monophyletic group supported by a 100 % bootstrap value and composed of mainly epiphytic species. Conclusions This is the first report of non-lignified pectin-rich secondary cell walls in ferns. Based on our molecular analysis, we reject the hypothesis of parallel evolution of helical cell wall thickenings in Aspleniaceae. Helical cell wall thickenings can mechanically stabilize the cortex tissue, allowing maximal uptake of water and nutrients during rainfall events. In addition, it can also act as a boundary layer increasing the diffusive pathway towards the atmosphere, preventing desiccation of the stele of epiphytic growing species. PMID:21118842

Use of a synchronization card for XMCD measurements at the XMaS Beamline

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

Bouchenoire, L.; Brown, S. D.; Thompson, P. B. J.

X-ray Magnetic Circular Dichroism (XMCD) spectra from a 5 {mu}m polycrystalline Gd foil were measured in transmission across the Gd L{sub 2,3} edges using the Multipurpose Unit for Synchronisation, Sequencing and Triggering (MUSST) card developed at the European Synchrotron Radiation Facility (ESRF). The circularly polarized x-rays were produced by a diamond phase-plate and their helicity was rapidly reversed through the use of a piezo driven device. The signal measured for each helicity was recorded by the MUSST card synchronized to the helicity reversal. The results are compared to those obtained using an analogue lock-in technique.

Use of a synchronization card for XMCD measurements at the XMaS Beamline

NASA Astrophysics Data System (ADS)

Bouchenoire, L.; Brown, S. D.; Thompson, P. B. J.; Hase, T. P. A.; Normile, P.; Bikondoa, O.; Hino, R.; Guijarro, M.; Stewart, M.; Cain, M. G.; Kervin, J.

2010-06-01

X-ray Magnetic Circular Dichroism (XMCD) spectra from a 5 μm polycrystalline Gd foil were measured in transmission across the Gd L2,3 edges using the Multipurpose Unit for Synchronisation, Sequencing and Triggering (MUSST) card developed at the European Synchrotron Radiation Facility (ESRF). The circularly polarized x-rays were produced by a diamond phase-plate and their helicity was rapidly reversed through the use of a piezo driven device. The signal measured for each helicity was recorded by the MUSST card synchronized to the helicity reversal. The results are compared to those obtained using an analogue lock-in technique.

Turbomachinery Laboratory Texas A and M University research progress on annular gas seals

NASA Technical Reports Server (NTRS)

Childs, Dara W.

1994-01-01

Three helically-grooved seals were tested and the results were compared to the MTI code SPIRALG. A smooth annular seal was tested at six eccentricity ratios from 0 to 0.5. The following are concluded in this viewgraph presentation: (1) Helical-grooved seals provide a substantial reduction in cross-coupled stiffness coefficients. Negative k(sub xy) values are obtained for no-swirl or low-swirl cases. (2) SPIRALG is completely unsuitable for the type of seal tested, namely, turbulent flow, wide grooves and lands, etc. (3) A good analysis code is needed to guide the design of helically-grooved annular seals including groove and smooth sections.

Spin dynamics in helical molecules with nonlinear interactions

NASA Astrophysics Data System (ADS)

Díaz, E.; Albares, P.; Estévez, P. G.; Cerveró, J. M.; Gaul, C.; Diez, E.; Domínguez-Adame, F.

2018-04-01

It is widely admitted that the helical conformation of certain chiral molecules may induce a sizable spin selectivity observed in experiments. Spin selectivity arises as a result of the interplay between a helicity-induced spin–orbit coupling (SOC) and electric dipole fields in the molecule. From the theoretical point of view, different phenomena might affect the spin dynamics in helical molecules, such as quantum dephasing, dissipation and the role of metallic contacts. With a few exceptions, previous studies usually neglect the local deformation of the molecule about the carrier, but this assumption seems unrealistic to describe charge transport in molecular systems. We introduce an effective model describing the electron spin dynamics in a deformable helical molecule with weak SOC. We find that the electron–lattice interaction allows the formation of stable solitons such as bright solitons with well defined spin projection onto the molecule axis. We present a thorough study of these bright solitons and analyze their possible impact on the spin dynamics in deformable helical molecules.

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.

Iron(II) supramolecular helicates interfere with the HIV-1 Tat–TAR RNA interaction critical for viral replication

PubMed Central

Malina, Jaroslav; Hannon, Michael J.; Brabec, Viktor

2016-01-01

The interaction between the HIV-1 transactivator protein Tat and TAR (transactivation responsive region) RNA, plays a critical role in HIV-1 transcription. Iron(II) supramolecular helicates were evaluated for their in vitro activity to inhibit Tat–TAR RNA interaction using UV melting studies, electrophoretic mobility shift assay, and RNase A footprinting. The results demonstrate that iron(II) supramolecular helicates inhibit Tat-TAR interaction at nanomolar concentrations by binding to TAR RNA. These studies provide a new insight into the biological potential of metallosupramolecular helicates. PMID:27405089

A field theory approach to the evolution of canonical helicity and energy

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

You, S.

A redefinition of the Lagrangian of a multi-particle system in fields reformulates the single-particle, kinetic, and fluid equations governing fluid and plasma dynamics as a single set of generalized Maxwell's equations and Ohm's law for canonical force-fields. The Lagrangian includes new terms representing the coupling between the motion of particle distributions, between distributions and electromagnetic fields, with relativistic contributions. The formulation shows that the concepts of self-organization and canonical helicity transport are applicable across single-particle, kinetic, and fluid regimes, at classical and relativistic scales. The theory gives the basis for comparing canonical helicity change to energy change in general systems.more » For example, in a fixed, isolated system subject to non-conservative forces, a species' canonical helicity changes less than total energy only if gradients in density or distribution function are shallow.« less

The helical structure of DNA facilitates binding

NASA Astrophysics Data System (ADS)

Berg, Otto G.; Mahmutovic, Anel; Marklund, Emil; Elf, Johan

2016-09-01

The helical structure of DNA imposes constraints on the rate of diffusion-limited protein binding. Here we solve the reaction-diffusion equations for DNA-like geometries and extend with simulations when necessary. We find that the helical structure can make binding to the DNA more than twice as fast compared to a case where DNA would be reactive only along one side. We also find that this rate advantage remains when the contributions from steric constraints and rotational diffusion of the DNA-binding protein are included. Furthermore, we find that the association rate is insensitive to changes in the steric constraints on the DNA in the helix geometry, while it is much more dependent on the steric constraints on the DNA-binding protein. We conclude that the helical structure of DNA facilitates the nonspecific binding of transcription factors and structural DNA-binding proteins in general.

Extended volume coverage in helical cone-beam CT by using PI-line based BPF algorithm

NASA Astrophysics Data System (ADS)

Cho, Seungryong; Pan, Xiaochuan

2007-03-01

We compared data requirements of filtered-backprojection (FBP) and backprojection-filtration (BPF) algorithms based on PI-lines in helical cone-beam CT. Since the filtration process in FBP algorithm needs all the projection data of PI-lines for each view, the required detector size should be bigger than the size that can cover Tam-Danielsson (T-D) window to avoid data truncation. BPF algorithm, however, requires the projection data only within the T-D window, which means smaller detector size can be used to reconstruct the same image than that in FBP. In other words, a longer helical pitch can be obtained by using BPF algorithm without any truncation artifacts when a fixed detector size is given. The purpose of the work is to demonstrate numerically that extended volume coverage in helical cone-beam CT by using PI-line-based BPF algorithm can be achieved.

Monte Carlo simulations of adult and pediatric computed tomography exams: Validation studies of organ doses with physical phantoms

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

Long, Daniel J.; Lee, Choonsik; Tien, Christopher

2013-01-15

Purpose: To validate the accuracy of a Monte Carlo source model of the Siemens SOMATOM Sensation 16 CT scanner using organ doses measured in physical anthropomorphic phantoms. Methods: The x-ray output of the Siemens SOMATOM Sensation 16 multidetector CT scanner was simulated within the Monte Carlo radiation transport code, MCNPX version 2.6. The resulting source model was able to perform various simulated axial and helical computed tomographic (CT) scans of varying scan parameters, including beam energy, filtration, pitch, and beam collimation. Two custom-built anthropomorphic phantoms were used to take dose measurements on the CT scanner: an adult male and amore » 9-month-old. The adult male is a physical replica of University of Florida reference adult male hybrid computational phantom, while the 9-month-old is a replica of University of Florida Series B 9-month-old voxel computational phantom. Each phantom underwent a series of axial and helical CT scans, during which organ doses were measured using fiber-optic coupled plastic scintillator dosimeters developed at University of Florida. The physical setup was reproduced and simulated in MCNPX using the CT source model and the computational phantoms upon which the anthropomorphic phantoms were constructed. Average organ doses were then calculated based upon these MCNPX results. Results: For all CT scans, good agreement was seen between measured and simulated organ doses. For the adult male, the percent differences were within 16% for axial scans, and within 18% for helical scans. For the 9-month-old, the percent differences were all within 15% for both the axial and helical scans. These results are comparable to previously published validation studies using GE scanners and commercially available anthropomorphic phantoms. Conclusions: Overall results of this study show that the Monte Carlo source model can be used to accurately and reliably calculate organ doses for patients undergoing a variety of axial or helical CT examinations on the Siemens SOMATOM Sensation 16 scanner.« less

Biomechanical evaluation of potential damage to hernia repair materials due to fixation with helical titanium tacks.

PubMed

Lerdsirisopon, Sopon; Frisella, Margaret M; Matthews, Brent D; Deeken, Corey R

2011-12-01

This study aimed to determine whether the strength and extensibility of hernia repair materials are negatively influenced by the application of helical titanium tacks. This study evaluated 14 meshes including bare polypropylene, macroporous polytetrafluoroethylene, absorbable barrier, partially absorbable mesh, and expanded polytetrafluoroethylene materials. Each mesh provided 15 specimens, which were prepared in 7.5 × 7.5-cm squares. Of these, 5 "undamaged" specimens were subjected to ball-burst testing to determine their biomechanical properties before application of helical titanium tacks (ProTack). To 10 "damaged" specimens 7 tacks were applied 1 cm apart in a 3.5-cm-diameter circle using a tacking force of 25 to 28 N. The tacks were removed from five of the specimens before ball-burst testing and left intact in the remaining five specimens. The application of tacks had no effect on the tensile strength of Dualmesh, ProLite Ultra, Infinit, Ultrapro, C-QUR Lite (<6 in.), Prolene Soft, or Physiomesh, but the tensile strengths were reduced for Bard Mesh, C-QUR, ProLite, and C-QUR Lite (>6 in.). Most of the meshes did not exhibit significantly different tensile strengths between removal of tacks and tacks left intact. Exceptions included C-QUR, Prolene, Ultrapro, and Bard Soft Mesh, which were weaker with removal of tacks than with tacks left intact during the test. Damage due to the application of helical titanium tacks also caused increased strain at a stress of 16 N/cm for all the meshes except C-QUR Lite (>6 in.) and Physiomesh. Many of the meshes evaluated in this study exhibited damage in the form of reduced tensile strength and increased extensibility after the application of tacks compared with the corresponding "undamaged" meshes. Meshes with smaller interstices and larger filaments were influenced negatively by the application of helical titanium tacks, whereas mesh designs with larger interstices and smaller filaments tended to maintain their baseline mechanical properties.

Matching into the Helical Bunch Coalescing Channel for a High Luminosity Muon Collider

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

Sy, Amy; Ankenbrandt, Charles; Derbenev, Yaroslav

2015-09-01

For high luminosity in a muon collider, muon bunches that have been cooled in the six-dimensional helical cooling channel (HCC) must be merged into a single bunch and further cooled in preparation for acceleration and transport to the collider ring. The helical bunch coalescing channel has been previously simulated and provides the most natural match from helical upstream and downstream subsystems. This work focuses on the matching from the exit of the multiple bunch HCC into the start of the helical bunch coalescing channel. The simulated helical matching section simultaneously matches the helical spatial period lambda in addition to providingmore » the necessary acceleration for efficient bunch coalescing. Previous studies assumed that the acceleration of muon bunches from p=209.15 MeV/c to 286.816 MeV/c and matching of lambda from 0.5 m to 1.0 m could be accomplished with zero particle losses and zero emittance growth in the individual bunches. This study demonstrates nonzero values for both particle loss and emittance growth, and provides considerations for reducing these adverse effects to best preserve high luminosity.« less

Enhanced heat transfer and frictional losses in heat exchanger tube with modified helical coiled inserts

NASA Astrophysics Data System (ADS)

Verma, Aditya; Kumar, Manoj; Patil, Anil Kumar

2018-04-01

The application of compact heat exchangers in any thermal system improves overall performance with a considerable reduction in size and weight. Inserts of different geometrical features have been used as turbulence promoting devices to increase the heat transfer rates. The present study deals with the experimental investigation of heat transfer and fluid flow characteristics of a tubular heat exchanger fitted with modified helical coiled inserts. Experiments have been carried out for a smooth tube without insert, tube fitted with helical coiled inserts, and modified helical coiled inserts. The helical coiled inserts are tested by varying the pitch ratio and wire diameter ratio from 0.5-1.5, and 0.063-0.125, respectively for the Reynolds number range of 1400 to 11,000. Experimental data have also been collected for the modified helical coiled inserts with gradually increasing pitch (GIP) and gradually decreasing pitch (GDP) configurations. The Nusselt number and friction factor values for helical coiled inserts are enhanced in the range of 1.42-2.62, 3.4-27.4, relative to smooth tube, respectively. The modified helical coiled insert showed enhancements in Nusselt number and friction factor values in the range of 1.49-3.14, 11.2-19.9, relative to smooth tube, respectively. The helical coiled and modified helical coiled inserts have thermo-hydraulic performance factor in the range of 0.59-1.29, 0.6-1.39, respectively. The empirical correlations of Nusselt number and friction factor for helical coiled inserts are proposed.

The Origins of Transmembrane Ion Channels

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Wilson, Michael A.

2012-01-01

Even though membrane proteins that mediate transport of ions and small molecules across cell walls are among the largest and least understood biopolymers in contemporary cells, it is still possible to shed light on their origins and early evolution. The central observation is that transmembrane portions of most ion channels are simply bundles of -helices. By combining results of experimental and computer simulation studies on synthetic models and natural channels, mostly of non-genomic origin, we show that the emergence of -helical channels was protobiologically plausible, and did not require highly specific amino acid sequences. Despite their simple structure, such channels could possess properties that, at the first sight, appear to require markedly larger complexity. Specifically, we explain how the antiamoebin channels, which are made of identical helices, 16 amino acids in length, achieve efficiency comparable to that of highly evolved channels. We further show that antiamoebin channels are extremely flexible, compared to modern, genetically coded channels. On the basis of our results, we propose that channels evolved further towards high structural complexity because they needed to acquire stable rigid structures and mechanisms for precise regulation rather than improve efficiency. In general, even though architectures of membrane proteins are not nearly as diverse as those of water-soluble proteins, they are sufficiently flexible to adapt readily to the functional demands arising during evolution.

An ESIPT fluorescent probe sensitive to protein α-helix structures.

PubMed

Jiang, Nan; Yang, Chanli; Dong, Xiongwei; Sun, Xianglang; Zhang, Dan; Liu, Changlin

2014-07-28

A large majority of membrane proteins have one or more transmembrane regions consisting of α-helices. Membrane protein levels differ from one type of cell to another, and the expression of membrane proteins also changes from normal to diseased cells. For example, prostate cancer cells have been reported to have downregulated expression of membrane proteins, including zinc transporters, compared with normal prostate cells. These reports inspired us to design a fluorescence probe sensitive to protein α-helical structures to discriminate individual prostate cancer cells from normal ones. A benzazole derivative ( in this study) was observed to emit strong fluorescence resulting from an excited-state intramolecular proton transfer (ESIPT) in protein α-helical environments. The intensity of ESIPT fluorescence of was observed to be positively correlated with the α-helix content of proteins. The molecular docking simulation suggested that it had low energy for the binding of to proteins when the binding sites were localized within the α-helical regions of protein via H-bonds. Furthermore, was found to be localized in cell membranes through binding to transmembrane α-helical regions of membrane proteins, and was capable of probing differences in the α-helix contents of membrane proteins between normal and cancerous prostate cells through changes in the ESIPT emission intensity. These results indicated that could distinguish individual prostate cancer cells from normal ones, as the changes in the ESIPT fluorescence intensity of could reflect the regulation in expression of the membrane proteins including zinc transporters. This recognition strategy of individual prostate cancer cells might contribute to early diagnosis techniques for prostate cancer.

Cervical helical axis characteristics and its center of rotation during active head and upper arm movements-comparisons of whiplash-associated disorders, non-specific neck pain and asymptomatic individuals.

PubMed

Grip, Helena; Sundelin, Gunnevi; Gerdle, Björn; Stefan Karlsson, J

2008-09-18

The helical axis model can be used to describe translation and rotation of spine segments. The aim of this study was to investigate the cervical helical axis and its center of rotation during fast head movements (side rotation and flexion/extension) and ball catching in patients with non-specific neck pain or pain due to whiplash injury as compared with matched controls. The aim was also to investigate correlations with neck pain intensity. A finite helical axis model with a time-varying window was used. The intersection point of the axis during different movement conditions was calculated. A repeated-measures ANOVA model was used to investigate the cervical helical axis and its rotation center for consecutive levels of 15 degrees during head movement. Irregularities in axis movement were derived using a zero-crossing approach. In addition, head, arm and upper body range of motion and velocity were observed. A general increase of axis irregularity that correlated to pain intensity was observed in the whiplash group. The rotation center was superiorly displaced in the non-specific neck pain group during side rotation, with the same tendency for the whiplash group. During ball catching, an anterior displacement (and a tendency to an inferior displacement) of the center of rotation and slower and more restricted upper body movements implied a changed movement strategy in neck pain patients, possibly as an attempt to stabilize the cervical spine during head movement.

Evolution of the baryon asymmetry through the electroweak crossover in the presence of a helical magnetic field

NASA Astrophysics Data System (ADS)

Kamada, Kohei; Long, Andrew J.

2016-12-01

We elaborate upon the model of baryogenesis from decaying magnetic helicity by focusing on the evolution of the baryon number and magnetic field through the Standard Model electroweak crossover. The baryon asymmetry is determined by a competition between the helical hypermagnetic field, which sources baryon number, and the electroweak sphaleron, which tends to wash out baryon number. At the electroweak crossover, both of these processes become inactive; the hypermagnetic field is converted into an electromagnetic field, which does not source baryon number, and the weak gauge boson masses grow, suppressing the electroweak sphaleron reaction. An accurate prediction of the relic baryon asymmetry requires a careful treatment of the crossover. We extend our previous study [K. Kamada and A. J. Long, Phys. Rev. D 94, 063501 (2016)], taking into account the gradual conversion of the hypermagnetic into the electromagnetic field. If the conversion is not completed by the time of sphaleron freeze-out, as both analytic and numerical studies suggest, the relic baryon asymmetry is enhanced compared to previous calculations. The observed baryon asymmetry of the Universe can be obtained for a primordial magnetic field that has a present-day field strength and coherence length of B0˜10-17 G and λ0˜10-3 pc and a positive helicity. For larger B0 the baryon asymmetry is overproduced, which may be in conflict with blazar observations that provide evidence for an intergalactic magnetic field of strength B0≳10-14 - 16 G .

On a Cyclic Variation of the Hemispheric Helicity Rule

NASA Technical Reports Server (NTRS)

Pevtsov, A. A.; Hagyard, M. J.; Blehm, Z.; Smith, J. E.; Canfield, R. C.; Sakurai, T.

2003-01-01

We report the result of a study magnetic helicity in solar active regions during 1980-2000.Using the vector magnetograms four different instruments we calculated the force-free parameter alpha as in Pevtsov et al.(1995). We use alpha as the proxy for current helicity density.

Effect of oscillation dynamics on long-range electron transfer in a helical peptide monolayer.

PubMed

Matsushita, Daisuke; Uji, Hirotaka; Kimura, Shunsaku

2018-06-06

Electron transfer (ET) reactions via helical peptides composed of -(Aib-Pro)n- were studied in self-assembled monolayers and compared with -(Ala-Aib)n- peptides. Short Aib-Pro peptides showed slightly higher ET rates due to the better electronic coupling of the Pro residue. But, the 24mer Aib-Pro peptide showed a smaller ET rate than the corresponding Ala-Aib peptide. On the basis of DFT calculations, the deceleration of the ET rate of the longer Aib-Pro peptide is considered to be due to the smaller number of active modes of accordion-like oscillations than the Ala-Aib peptide, which has a strong influence on a long-range ET reaction.

Studies of Solar Helicity Using Vector Magnetograms

NASA Technical Reports Server (NTRS)

Hagyard, Mona J.; Pevstov, Alexei A.

1999-01-01

observations of photospheric magnetic fields made with vector magnetographs have been used recently to study solar helicity. In this paper we indicate what can and cannot be derived from vector magnetograms, and point out some potential problems in these data that could affect the calculations of 'helicity'. Among these problems are magnetic saturation, Faraday rotation, low spectral resolution, and the method of resolving the ambiguity in the azimuth.

The National Lung Screening Trial (NLST) | Division of Cancer Prevention

Cancer.gov

The National Lung Screening Trial (NLST) compared two ways of detecting lung cancer: low-dose helical computed tomography (CT) and standard chest X-ray. Both chest X-rays and low-dose helical CT scans have been used to find lung cancer early, but the effects of these screening techniques on lung cancer mortality rates had not been determined. NLST enrolled 53,454 current or

THE EFFECTS OF SPATIAL SMOOTHING ON SOLAR MAGNETIC HELICITY PARAMETERS AND THE HEMISPHERIC HELICITY SIGN RULE

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

Ocker, Stella Koch; Petrie, Gordon, E-mail: socker@oberlin.edu, E-mail: gpetrie@nso.edu

The hemispheric preference for negative/positive helicity to occur in the northern/southern solar hemisphere provides clues to the causes of twisted, flaring magnetic fields. Previous studies on the hemisphere rule may have been affected by seeing from atmospheric turbulence. Using Hinode /SOT-SP data spanning 2006–2013, we studied the effects of two spatial smoothing tests that imitate atmospheric seeing: noise reduction by ignoring pixel values weaker than the estimated noise threshold, and Gaussian spatial smoothing. We studied in detail the effects of atmospheric seeing on the helicity distributions across various field strengths for active regions (ARs) NOAA 11158 and NOAA 11243, in addition tomore » studying the average helicities of 179 ARs with and without smoothing. We found that, rather than changing trends in the helicity distributions, spatial smoothing modified existing trends by reducing random noise and by regressing outliers toward the mean, or removing them altogether. Furthermore, the average helicity parameter values of the 179 ARs did not conform to the hemisphere rule: independent of smoothing, the weak-vertical-field values tended to be negative in both hemispheres, and the strong-vertical-field values tended to be positive, especially in the south. We conclude that spatial smoothing does not significantly affect the overall statistics for space-based data, and thus seeing from atmospheric turbulence seems not to have significantly affected previous studies’ ground-based results on the hemisphere rule.« less

Structures of the transmembrane helices of the G-protein coupled receptor, rhodopsin.

PubMed

Katragadda, M; Chopra, A; Bennett, M; Alderfer, J L; Yeagle, P L; Albert, A D

2001-07-01

An hypothesis is tested that individual peptides corresponding to the transmembrane helices of the membrane protein, rhodopsin, would form helices in solution similar to those in the native protein. Peptides containing the sequences of helices 1, 4 and 5 of rhodopsin were synthesized. Two peptides, with overlapping sequences at their termini, were synthesized to cover each of the helices. The peptides from helix 1 and helix 4 were helical throughout most of their length. The N- and C-termini of all the peptides were disordered and proline caused opening of the helical structure in both helix 1 and helix 4. The peptides from helix 5 were helical in the middle segment of each peptide, with larger disordered regions in the N- and C-termini than for helices 1 and 4. These observations show that there is a strong helical propensity in the amino acid sequences corresponding to the transmembrane domain of this G-protein coupled receptor. In the case of the peptides from helix 4, it was possible to superimpose the structures of the overlapping sequences to produce a construct covering the whole of the sequence of helix 4 of rhodopsin. As similar superposition for the peptides from helix 1 also produced a construct, but somewhat less successfully because of the disordering in the region of sequence overlap. This latter problem was more severe for helix 5 and therefore a single peptide was synthesized for the entire sequence of this helix, and its structure determined. It proved to be helical throughout. Comparison of all these structures with the recent crystal structure of rhodopsin revealed that the peptide structures mimicked the structures seen in the whole protein. Thus similar studies of peptides may provide useful information on the secondary structure of other transmembrane proteins built around helical bundles.

The next large helical devices

NASA Astrophysics Data System (ADS)

Iiyoshi, Atsuo; Yamazaki, Kozo

1995-06-01

Helical systems have the strong advantage of inherent steady-state operation for fusion reactors. Two large helical devices with fully superconducting coil systems are presently under design and construction. One is the LHD (Large Helical Device) [Fusion Technol. 17, 169 (1990)] with major radius=3.9 m and magnetic field=3-4 T, that is under construction during 1990-1997 at NIFS (National Institute for Fusion Science), Nagoya/Toki, Japan; it features continuous helical coils and a clean helical divertor focusing on edge configuration optimization. The other one in the W7-X (Wendelstein 7-X) [in Plasma Physics and Controlled Fusion Nuclear Research, 1990, (International Atomic Energy Agency, Vienna, 1991), Vol. 3, p. 525] with major radius=5.5 m and magnetic field=3 T, that is under review at IPP (Max-Planck Institute for Plasma Physics), Garching, Germany; it has adopted a modular coil system after elaborate optimization studies. These two programs are complementary in promoting world helical fusion research and in extending the understanding of toroidal plasmas through comparisons with large tokamaks.

Pulling helices inside bacteria: imperfect helices and rings

NASA Astrophysics Data System (ADS)

Rutenberg, Andrew; Allard, Jun

2009-03-01

We study steady-state configurations of intrinsically-straight elastic filaments constrained within rod-shaped bacteria that have applied forces distributed along their length. Perfect steady-state helices result from axial or azimuthal forces applied at filament ends, however azimuthal forces are required for the small pitches observed for MreB filaments within bacteria. Helix-like configurations can result from distributed forces, including co-existence between rings and imperfect helices. Levels of expression and/or bundling of the polymeric protein could mediate this co-existence.

Pulling Helices inside Bacteria: Imperfect Helices and Rings

NASA Astrophysics Data System (ADS)

Allard, Jun F.; Rutenberg, Andrew D.

2009-04-01

We study steady-state configurations of intrinsically-straight elastic filaments constrained within rod-shaped bacteria that have applied forces distributed along their length. Perfect steady-state helices result from axial or azimuthal forces applied at filament ends, however azimuthal forces are required for the small pitches observed for MreB filaments within bacteria. Helix-like configurations can result from distributed forces, including coexistence between rings and imperfect helices. Levels of expression and/or bundling of the polymeric protein could mediate this coexistence.

Chiral Sulfoxide-Induced Single Turn Peptide α-Helicity

PubMed Central

Zhang, Qingzhou; Jiang, Fan; Zhao, Bingchuan; Lin, Huacan; Tian, Yuan; Xie, Mingsheng; Bai, Guoyun; Gilbert, Adam M.; Goetz, Gilles H.; Liras, Spiros; Mathiowetz, Alan A.; Price, David A.; Song, Kun; Tu, Meihua; Wu, Yujie; Wang, Tao; Flanagan, Mark E.; Wu, Yun-Dong; Li, Zigang

2016-01-01

Inducing α-helicity through side-chain cross-linking is a strategy that has been pursued to improve peptide conformational rigidity and bio-availability. Here we describe the preparation of small peptides tethered to chiral sulfoxide-containing macrocyclic rings. Furthermore, a study of structure-activity relationships (SARs) disclosed properties with respect to ring size, sulfur position, oxidation state, and stereochemistry that show a propensity to induce α-helicity. Supporting data include circular dichroism spectroscopy (CD), NMR spectroscopy, and a single crystal X-ray structure for one such stabilized peptide. Finally, theoretical studies are presented to elucidate the effect of chiral sulfoxides in inducing backbone α-helicity. PMID:27934919

Comparative study of protein unfolding in aqueous urea and dimethyl sulfoxide solutions: surface polarity, solvent specificity, and sequence of secondary structure melting.

PubMed

Roy, Susmita; Bagchi, Biman

2014-05-29

Elucidation of possible pathways between folded (native) and unfolded states of a protein is a challenging task, as the intermediates are often hard to detect. Here, we alter the solvent environment in a controlled manner by choosing two different cosolvents of water, urea, and dimethyl sulfoxide (DMSO) and study unfolding of four different proteins to understand the respective sequence of melting by computer simulation methods. We indeed find interesting differences in the sequence of melting of α helices and β sheets in these two solvents. For example, in 8 M urea solution, β-sheet parts of a protein are found to unfold preferentially, followed by the unfolding of α helices. In contrast, 8 M DMSO solution unfolds α helices first, followed by the separation of β sheets for the majority of proteins. Sequence of unfolding events in four different α/β proteins and also in chicken villin head piece (HP-36) both in urea and DMSO solutions demonstrate that the unfolding pathways are determined jointly by relative exposure of polar and nonpolar residues of a protein and the mode of molecular action of a solvent on that protein.

Comparison of orbital volume obtained by tomography and rapid prototyping.

PubMed

Roça, Guilherme Berto; Foggiatto, José Aguiomar; Ono, Maria Cecilia Closs; Ono, Sergio Eiji; da Silva Freitas, Renato

2013-11-01

This study aims to compare orbital volume obtained by helical tomography and rapid prototyping. The study sample was composed of 6 helical tomography scans. Eleven healthy orbits were identified to have their volumes measured. The volumetric analysis with the helical tomography utilized the same protocol developed by the Plastic Surgery Unit of the Federal University of Paraná. From the CT images, 11 prototypes were created, and their respective volumes were analyzed in 2 ways: using software by SolidWorks and by direct analysis, when the prototype was filled with saline solution. For statistical analysis, the results of the volumes of the 11 orbits were considered independent. The average orbital volume measurements obtained by the method of Ono et al was 20.51 cm, the average obtained by the SolidWorks program was 20.64 cm, and the average measured using the prototype method was 21.81 cm. The 3 methods demonstrated a strong correlation between the measurements. The right and left orbits of each patient had similar volumes. The tomographic method for the analysis of orbital volume using the Ono protocol yielded consistent values, and by combining this method with rapid prototyping, both reliability validations of results were enhanced.

[Comparison of radiation dose reduction of prospective ECG-gated one beat scan using 320 area detector CT coronary angiography and prospective ECG-gated helical scan with high helical pitch (FlashScan) using 64 multidetector-row CT coronary angiography].

PubMed

Matsutani, Hideyuki; Sano, Tomonari; Kondo, Takeshi; Fujimoto, Shinichiro; Sekine, Takako; Arai, Takehiro; Morita, Hitomi; Takase, Shinichi

2010-12-20

A high radiation dose associated with 64 multidetector-row computed tomography (64-MDCT) is a major concern for physicians and patients alike. A new 320 row area detector computed tomography (ADCT) can obtain a view of the entire heart with one rotation (0.35 s) without requiring the helical method. As such, ADCT is expected to reduce the radiation dose. We studied image quality and radiation dose of ADCT compared to that of 64-MDCT in patients with a low heart rate (HR≤60). Three hundred eighty-five consecutive patients underwent 64-MDCT and 379 patients, ADCT. Patients with an arrhythmia were excluded. Prospective ECG-gated helical scan with high HP (FlashScan) in 64 was used for MDCT and prospective ECG-gated conventional one beat scan, for 320-ADCT. Image quality was visually evaluated by an image quality score. Radiation dose was estimated by DLP (mGy･cm) for 64-MDCT and DLP.e (mGy･cm) for 320-ADCT. Radiation dose of 320-ADCT (208±48 mGy･cm) was significantly (P<0.0001) lower than that of 64-MDCT (484±112 mGy･cm), and image quality score of 320-ADCT (3.0±0.2) was significantly (P=0.0011) higher than that of 64-MDCT (2.9±0.4). Scan time of 320-ADCT (1.4±0.1 s) was also significantly (P<0.0001) shorter than that of 64-MDCT (6.8±0.6 s). 320-ADCT can achieve not only a reduction in radiation dose but also a superior image quality and shortening of scan time compared to 64-MDCT.

A Cobalt Supramolecular Triple-Stranded Helicate-based Discrete Molecular Cage

PubMed Central

Mai, Hien Duy; Kang, Philjae; Kim, Jin Kyung; Yoo, Hyojong

2017-01-01

We report a strategy to achieve a discrete cage molecule featuring a high level of structural hierarchy through a multiple-assembly process. A cobalt (Co) supramolecular triple-stranded helicate (Co-TSH)-based discrete molecular cage (1) is successfully synthesized and fully characterized. The solid-state structure of 1 shows that it is composed of six triple-stranded helicates interconnected by four linking cobalt species. This is an unusual example of a highly symmetric cage architecture resulting from the coordination-driven assembly of metallosupramolecular modules. The molecular cage 1 shows much higher CO2 uptake properties and selectivity compared with the separate supramolecular modules (Co-TSH, complex 2) and other molecular platforms. PMID:28262690

A tendril perversion in a helical oligomer: trapping and characterizing a mobile screw-sense reversal† †Electronic supplementary information (ESI) available. CCDC X-ray crystal data for 1a and 1b have been deposited with the CCDC, deposition numbers 1518806 and 1518807. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c6sc05474a Click here for additional data file. Click here for additional data file.

PubMed Central

Tomsett, Michael; Maffucci, Irene; Le Bailly, Bryden A. F.; Byrne, Liam; Bijvoets, Stefan M.; Lizio, M. Giovanna; Raftery, James; Butts, Craig P.; Webb, Simon J.; Contini, Alessandro

2017-01-01

Helical oligomers of achiral monomers adopt domains of uniform screw sense, which are occasionally interrupted by screw-sense reversals. These rare, elusive, and fast-moving features have eluded detailed characterization. We now describe the structure and habits of a screw-sense reversal trapped within a fragment of a helical oligoamide foldamer of the achiral quaternary amino acid 2-aminoisobutyric acid (Aib). The reversal was enforced by compelling the amide oligomer to adopt a right-handed screw sense at one end and a left-handed screw sense at the other. The trapped reversal was characterized by X-ray crystallography, and its dynamic properties were monitored by NMR and circular dichroism, and modelled computationally. Raman spectroscopy indicated that a predominantly helical architecture was maintained despite the reversal. NMR and computational results indicated a stepwise shift from one screw sense to another on moving along the helical chain, indicating that in solution the reversal is not localised at a specific location, but is free to migrate across a number of residues. Analogous unconstrained screw-sense reversals that are free to move within a helical structure are likely to provide the mechanism by which comparable helical polymers and foldamers undergo screw-sense inversion. PMID:28451368

Spectroscopic studies of bacteriorhodopsin fragments dissolved in organic solution.

PubMed Central

Torres, J; Padrós, E

1995-01-01

Fourier transform infrared and UV fourth-derivative spectroscopies were used to study the secondary structure of bacteriorhodopsin and its chymotryptic and one of the sodium borohydride fragments dissolved in chloroform-methanol (1:1, v/v), 0.1 M LiClO4. The C1 fragment (helices C, D, E, F, and G) showed an alpha-helical content of about 53%, whereas C2 (helices A and B) had about 60%, and B2 (helices F and G) about 65% alpha-helix. The infrared main band indicated differences in alpha-helical properties between these fragments. These techniques were also used to obtain information on the interactions among helices. According to the results obtained from the hydrogen/deuterium exchange kinetics, about 40% of the amide protons of C2 are particularly protected against exchange, whereas for the C1 fragment this process is unexpectedly fast. UV fourth-derivative spectra of these samples were used to obtain information about the environment of Trp side chains. The results showed that the Trp residues of C2 are more shielded from the solvent than those of C1 or B2. The results of this work indicate that the specific interactions existing between the transmembrane segments induce different types of helical conformations in native bacteriorhodopsin. PMID:7612847

Influence of helical external driven current on nonlinear resistive tearing mode evolution and saturation in tokamaks

NASA Astrophysics Data System (ADS)

Zhang, W.; Wang, S.; Ma, Z. W.

2017-06-01

The influences of helical driven currents on nonlinear resistive tearing mode evolution and saturation are studied by using a three-dimensional toroidal resistive magnetohydrodynamic code (CLT). We carried out three types of helical driven currents: stationary, time-dependent amplitude, and thickness. It is found that the helical driven current is much more efficient than the Gaussian driven current used in our previous study [S. Wang et al., Phys. Plasmas 23(5), 052503 (2016)]. The stationary helical driven current cannot persistently control tearing mode instabilities. For the time-dependent helical driven current with f c d = 0.01 and δ c d < 0.04 , the island size can be reduced to its saturated level that is about one third of the initial island size. However, if the total driven current increases to about 7% of the total plasma current, tearing mode instabilities will rebound again due to the excitation of the triple tearing mode. For the helical driven current with time dependent strength and thickness, the reduction speed of the radial perturbation component of the magnetic field increases with an increase in the driven current and then saturates at a quite low level. The tearing mode is always controlled even for a large driven current.

Maintenance of electrostatic stabilization in altered tubulin lateral contacts may facilitate formation of helical filaments in foraminifera.

PubMed

Bassen, David M; Hou, Yubo; Bowser, Samuel S; Banavali, Nilesh K

2016-08-19

Microtubules in foraminiferan protists (forams) can convert into helical filament structures, in which longitudinal intraprotofilament interactions between tubulin heterodimers are thought to be lost, while lateral contacts across protofilaments are still maintained. The coarse geometric features of helical filaments are known through low-resolution negative stain electron microscopy (EM). In this study, geometric restraints derived from these experimental data were used to generate an average atomic-scale helical filament model, which anticipated a modest reorientation in the lateral tubulin heterodimer interface. Restrained molecular dynamics (MD) simulations of the nearest neighbor interactions combined with a Genalized Born implicit solvent model were used to assess the lateral, longitudinal, and seam contacts in 13-3 microtubules and the reoriented lateral contacts in the helical filament model. This electrostatic analysis suggests that the change in the lateral interface in the helical filament does not greatly diminish the lateral electrostatic interaction. After longitudinal dissociation, the 13-3 seam interaction is much weaker than the reoriented lateral interface in the helical filament model, providing a plausible atomic-detail explanation for seam-to-lateral contact transition that enables the transition to a helical filament structure.

Maintenance of electrostatic stabilization in altered tubulin lateral contacts may facilitate formation of helical filaments in foraminifera

NASA Astrophysics Data System (ADS)

Bassen, David M.; Hou, Yubo; Bowser, Samuel S.; Banavali, Nilesh K.

2016-08-01

Microtubules in foraminiferan protists (forams) can convert into helical filament structures, in which longitudinal intraprotofilament interactions between tubulin heterodimers are thought to be lost, while lateral contacts across protofilaments are still maintained. The coarse geometric features of helical filaments are known through low-resolution negative stain electron microscopy (EM). In this study, geometric restraints derived from these experimental data were used to generate an average atomic-scale helical filament model, which anticipated a modest reorientation in the lateral tubulin heterodimer interface. Restrained molecular dynamics (MD) simulations of the nearest neighbor interactions combined with a Genalized Born implicit solvent model were used to assess the lateral, longitudinal, and seam contacts in 13-3 microtubules and the reoriented lateral contacts in the helical filament model. This electrostatic analysis suggests that the change in the lateral interface in the helical filament does not greatly diminish the lateral electrostatic interaction. After longitudinal dissociation, the 13-3 seam interaction is much weaker than the reoriented lateral interface in the helical filament model, providing a plausible atomic-detail explanation for seam-to-lateral contact transition that enables the transition to a helical filament structure.

Theoretical model of chirality-induced helical self-propulsion

NASA Astrophysics Data System (ADS)

Yamamoto, Takaki; Sano, Masaki

2018-01-01

We recently reported the experimental realization of a chiral artificial microswimmer exhibiting helical self-propulsion [T. Yamamoto and M. Sano, Soft Matter 13, 3328 (2017), 10.1039/C7SM00337D]. In the experiment, cholesteric liquid crystal (CLC) droplets dispersed in surfactant solutions swam spontaneously, driven by the Marangoni flow, in helical paths whose handedness is determined by the chirality of the component molecules of CLC. To study the mechanism of the emergence of the helical self-propelled motion, we propose a phenomenological model of the self-propelled helical motion of the CLC droplets. Our model is constructed by symmetry argument in chiral systems, and it describes the dynamics of CLC droplets with coupled time-evolution equations in terms of a velocity, an angular velocity, and a tensor variable representing the symmetry of the helical director field of the droplet. We found that helical motions as well as other chiral motions appear in our model. By investigating bifurcation behaviors between each chiral motion, we found that the chiral coupling terms between the velocity and the angular velocity, the structural anisotropy of the CLC droplet, and the nonlinearity of model equations play a crucial role in the emergence of the helical motion of the CLC droplet.

PI-line-based image reconstruction in helical cone-beam computed tomography with a variable pitch.

PubMed

Zou, Yu; Pan, Xiaochuan; Xia, Dan; Wang, Ge

2005-08-01

Current applications of helical cone-beam computed tomography (CT) involve primarily a constant pitch where the translating speed of the table and the rotation speed of the source-detector remain constant. However, situations do exist where it may be more desirable to use a helical scan with a variable translating speed of the table, leading a variable pitch. One of such applications could arise in helical cone-beam CT fluoroscopy for the determination of vascular structures through real-time imaging of contrast bolus arrival. Most of the existing reconstruction algorithms have been developed only for helical cone-beam CT with constant pitch, including the backprojection-filtration (BPF) and filtered-backprojection (FBP) algorithms that we proposed previously. It is possible to generalize some of these algorithms to reconstruct images exactly for helical cone-beam CT with a variable pitch. In this work, we generalize our BPF and FBP algorithms to reconstruct images directly from data acquired in helical cone-beam CT with a variable pitch. We have also performed a preliminary numerical study to demonstrate and verify the generalization of the two algorithms. The results of the study confirm that our generalized BPF and FBP algorithms can yield exact reconstruction in helical cone-beam CT with a variable pitch. It should be pointed out that our generalized BPF algorithm is the only algorithm that is capable of reconstructing exactly region-of-interest image from data containing transverse truncations.

Aortic Valve Stenosis Increases Helical Flow and Flow Complexity: A Study of Intra-Operative Cardiac Vector Flow Imaging.

PubMed

Hansen, Kristoffer Lindskov; Møller-Sørensen, Hasse; Kjaergaard, Jesper; Jensen, Maiken Brit; Jensen, Jørgen Arendt; Nielsen, Michael Bachmann

2017-08-01

Aortic valve stenosis alters blood flow in the ascending aorta. Using intra-operative vector flow imaging on the ascending aorta, secondary helical flow during peak systole and diastole, as well as flow complexity of primary flow during systole, were investigated in patients with normal, stenotic and replaced aortic valves. Peak systolic helical flow, diastolic helical flow and flow complexity during systole differed between the groups (p < 0.0001), and correlated to peak systolic velocity (R = 0.94, 0.87 and 0.88, respectively). The study indicates that aortic valve stenosis increases helical flow and flow complexity, which are measurable with vector flow imaging. For assessment of aortic stenosis and optimization of valve surgery, vector flow imaging may be useful. Copyright © 2017 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

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

Bidirectional helical motility of cytoplasmic dynein around microtubules

PubMed Central

Can, Sinan; Dewitt, Mark A; Yildiz, Ahmet

2014-01-01

Cytoplasmic dynein is a molecular motor responsible for minus-end-directed cargo transport along microtubules (MTs). Dynein motility has previously been studied on surface-immobilized MTs in vitro, which constrains the motors to move in two dimensions. In this study, we explored dynein motility in three dimensions using an MT bridge assay. We found that dynein moves in a helical trajectory around the MT, demonstrating that it generates torque during cargo transport. Unlike other cytoskeletal motors that produce torque in a specific direction, dynein generates torque in either direction, resulting in bidirectional helical motility. Dynein has a net preference to move along a right-handed helical path, suggesting that the heads tend to bind to the closest tubulin binding site in the forward direction when taking sideways steps. This bidirectional helical motility may allow dynein to avoid roadblocks in dense cytoplasmic environments during cargo transport. DOI: http://dx.doi.org/10.7554/eLife.03205.001 PMID:25069614

Studies on convective heat transfer through helical coils

NASA Astrophysics Data System (ADS)

Pawar, S. S.; Sunnapwar, Vivek K.

2013-12-01

An experimental investigation on steady state convection heat transfer from vertical helical coiled tubes in water was performed for laminar flow regime. Three coils with curvature ratios as 0.0757, 0.064, 0.055 and range of Prandtl number from 3.81 to 4.8, Reynolds number from 3,166 to 9,658 were considered in this work. The heat transfer data were generated from 30 experiments conducted at constant water bath temperature (60 °C) for different cold water flow rates in helical coils. For the first time, an innovative approach of correlating Nusselt number with ‘M’ number is proposed which is not available in the literature and the developed correlations are found to be in good agreement with the work of earlier researchers. Thus, dimensionless number ‘M’ was found to be significant to characterize the hydrodynamics of fluid flow and heat transfer correlations in helical coils. Several other correlations based on experimental data are developed. To cover wide range of industrial applications, suitable generalized correlations based on extended parameters beyond the range of present experimental work are also developed. All these correlations are developed by using least-squares power law fit and multiple-regression analysis of MATLAB software. Correlations so developed were compared with published correlations and were found to be in good agreement. Comparison of heat transfer coefficients, friction factor and Nusselt number for different geometrical conditions is presented in this paper.

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.

Structure and interactions of biological helices

NASA Astrophysics Data System (ADS)

Kornyshev, Alexei A.; Lee, Dominic J.; Leikin, Sergey; Wynveen, Aaron

2007-07-01

Helices are essential building blocks of living organisms, be they molecular fragments of proteins ( α -helices), macromolecules (DNA and collagen), or multimolecular assemblies (microtubules and viruses). Their interactions are involved in packing of meters of genetic material within cells and phage heads, recognition of homologous genes in recombination and DNA repair, stability of tissues, and many other processes. Helical molecules form a variety of mesophases in vivo and in vitro. Recent structural studies, direct measurements of intermolecular forces, single-molecule manipulations, and other experiments have accumulated a wealth of information and revealed many puzzling physical phenomena. It is becoming increasingly clear that in many cases the physics of biological helices cannot be described by theories that treat them as simple, unstructured polyelectrolytes. The present article focuses on the most important and interesting aspects of the physics of structured macromolecules, highlighting various manifestations of the helical motif in their structure, elasticity, interactions with counterions, aggregation, and poly- and mesomorphic transitions.

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.

WE-G-18A-06: Sinogram Restoration in Helical Cone-Beam CT

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

Little, K; Riviere, P La

2014-06-15

Purpose: To extend CT sinogram restoration, which has been shown in 2D to reduce noise and to correct for geometric effects and other degradations at a low computational cost, from 2D to a 3D helical cone-beam geometry. Methods: A method for calculating sinogram degradation coefficients for a helical cone-beam geometry was proposed. These values were used to perform penalized-likelihood sinogram restoration on simulated data that were generated from the FORBILD thorax phantom. Sinogram restorations were performed using both a quadratic penalty and the edge-preserving Huber penalty. After sinogram restoration, Fourier-based analytical methods were used to obtain reconstructions. Resolution-variance trade-offs weremore » investigated for several locations within the reconstructions for the purpose of comparing sinogram restoration to no restoration. In order to compare potential differences, reconstructions were performed using different groups of neighbors in the penalty, two analytical reconstruction methods (Katsevich and single-slice rebinning), and differing helical pitches. Results: The resolution-variance properties of reconstructions restored using sinogram restoration with a Huber penalty outperformed those of reconstructions with no restoration. However, the use of a quadratic sinogram restoration penalty did not lead to an improvement over performing no restoration at the outer regions of the phantom. Application of the Huber penalty to neighbors both within a view and across views did not perform as well as only applying the penalty to neighbors within a view. General improvements in resolution-variance properties using sinogram restoration with the Huber penalty were not dependent on the reconstruction method used or the magnitude of the helical pitch. Conclusion: Sinogram restoration for noise and degradation effects for helical cone-beam CT is feasible and should be able to be applied to clinical data. When applied with the edge-preserving Huber penalty, sinogram restoration leads to an improvement in resolution-variance tradeoffs.« less

Structural propensities and entropy effects in peptide helix-coil transitions

NASA Astrophysics Data System (ADS)

Chemmama, Ilan E.; Pelea, Adam Colt; Bhandari, Yuba R.; Chapagain, Prem P.; Gerstman, Bernard S.

2012-09-01

The helix-coil transition in peptides is a critical structural transition leading to functioning proteins. Peptide chains have a large number of possible configurations that must be accounted for in statistical mechanical investigations. Using hydrogen bond and local helix propensity interaction terms, we develop a method for obtaining and incorporating the degeneracy factor that allows the exact calculation of the partition function for a peptide as a function of chain length. The partition function is used in calculations for engineered peptide chains of various lengths that allow comparison with a variety of different types of experimentally measured quantities, such as fraction of helicity as a function of both temperature and chain length, heat capacity, and denaturation studies. When experimental sensitivity in helicity measurements is properly accounted for in the calculations, the calculated curves fit well with the experimental curves. We determine values of interaction energies for comparison with known biochemical interactions, as well as quantify the difference in the number of configurations available to an amino acid in a random coil configuration compared to a helical configuration.

Moreau's hydrodynamic helicity and the life of vortex knots and links

NASA Astrophysics Data System (ADS)

Irvine, William T. M.

2018-03-01

This contribution to an issue of Comptes rendus Mécanique, commemorating the scientific work of Jean-Jacques Moreau (1923-2014), is intended to give a brief overview of recent developments in the study of helicity dynamics in real fluids and an outlook on the growing legacy of Moreau's work. Moreau's discovery of the conservation of hydrodynamic helicity, presented in an article in the Comptes rendus de l'Académie des sciences in 1961, was not recognized until long after it was published. This seminal contribution is gaining a new life now that modern developments allow the study of helicity and topology in fields and is having a growing impact on diverse areas of physics.

Multispectroscopic and Theoretical Exploration of the Comparative Binding Aspects of Bioflavonoid Fisetin with Triple- and Double-Helical Forms of RNA.

PubMed

Bhuiya, Sutanwi; Haque, Lucy; Goswami, Rapti; Das, Suman

2017-12-14

The interactions of RNA triplex (U.A*U) and duplex (A.U) with naturally occurring flavonoid fisetin (FTN) have been examined at pH 7.0 using various spectroscopic, viscometric, and theoretical studies. Experimental observations showed that the ligand binds with both double- and triple-helical forms of RNA, although the binding affinity is greater for the triplex structure (5.94 × 10 6 M -1 ) compared to that for the duplex counterpart (1.0 × 10 5 M -1 ). Thermal melting experiments revealed that the Hoogsteen base-paired third strand of triplex was stabilized to a greater extent (∼14 °C) compared with the Watson-Crick base-paired second strand (∼4 °C) in the presence of FTN. From fluorimetric study, we observed that U.A*U and A.U primarily bind to the photoproduced tautomer of FTN in the excited state. Steady-state and time-resolved anisotropy measurements illustrate considerable modulations of the spectroscopic properties of the tautomeric FTN within the RNA environment. Viscometric, fluorescence quenching, and thermal melting studies all together support the mode of binding to be intercalation. Theoretical study explains the experimental absorption and emission (dual fluorescence) behavior of FTN along with the excited-state intramolecular proton transfer process.

Chiral self-assembly of helical particles.

PubMed

Kolli, Hima Bindu; Cinacchi, Giorgio; Ferrarini, Alberta; Giacometti, Achille

2016-01-01

The shape of the building blocks plays a crucial role in directing self-assembly towards desired architectures. Out of the many different shapes, the helix has a unique position. Helical structures are ubiquitous in nature and a helical shape is exhibited by the most important biopolymers like polynucleotides, polypeptides and polysaccharides as well as by cellular organelles like flagella. Helical particles can self-assemble into chiral superstructures, which may have a variety of applications, e.g. as photonic (meta)materials. However, a clear and definite understanding of these structures has not been entirely achieved yet. We have recently undertaken an extensive investigation on the phase behaviour of hard helical particles, using numerical simulations and classical density functional theory. Here we present a detailed study of the phase diagram of hard helices as a function of their morphology. This includes a variety of liquid-crystal phases, with different degrees of orientational and positional ordering. We show how, by tuning the helix parameters, it is possible to control the organization of the system. Starting from slender helices, whose phase behaviour is similar to that of rodlike particles, an increase in curliness leads to the onset of azimuthal correlations between the particles and the formation of phases specific to helices. These phases feature a new kind of screw order, of which there is experimental evidence in colloidal suspensions of helical flagella.

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

Helical Spin Order from Topological Dirac and Weyl Semimetals

DOE PAGES

Sun, Xiao-Qi; Zhang, Shou-Cheng; Wang, Zhong

2015-08-14

In this paper, we study dynamical mass generation and the resultant helical spin orders in topological Dirac and Weyl semimetals, including the edge states of quantum spin Hall insulators, the surface states of weak topological insulators, and the bulk materials of Weyl semimetals. In particular, the helical spin textures of Weyl semimetals manifest the spin-momentum locking of Weyl fermions in a visible manner. Finally, the spin-wave fluctuations of the helical order carry electric charge density; therefore, the spin textures can be electrically controlled in a simple and predictable manner.

Improving cell penetration of helical peptides stabilized by N-terminal crosslinked aspartic acids.

PubMed

Zhao, Hui; Jiang, Yanhong; Tian, Yuan; Yang, Dan; Qin, Xuan; Li, Zigang

2017-01-04

Cell penetration and nucleus translocation efficiency are important for the cellular activities of peptide therapeutics. For helical peptides stabilized by N-terminal crosslinked aspartic acid, correlations between their penetration efficiency/nucleus translocation and physicochemical properties were studied. An increase in hydrophobicity and isoelectric point will promote cellular uptake and nucleus translocation of stabilized helices.

Effects of a spin-flavour-dependent interaction on light-flavoured baryon helicity amplitudes

NASA Astrophysics Data System (ADS)

Ronniger, Michael; Metsch, Bernard Ch.

2013-01-01

This paper is a continuation of a previous work about the effects of a phenomenological flavour-dependent force in a relativistically covariant constituent quark model based on the Salpeter equation on the structure of light-flavoured baryon resonances. Here the longitudinal and transverse helicity amplitudes as studied experimentally in the electro-excitation of nucleon- and Δ-resonances are calculated. In particular the amplitudes for the excitation of three- and four-star resonances as calculated in a previous model A are compared to those of the novel model C as well as to existing and partially new experimental data such as, e.g., determined by the CB-ELSA Collaboration. A brief discussion on some improvements to model C is given after the introduction.

Optically pure, water-stable metallo-helical ‘flexicate’ assemblies with antibiotic activity

NASA Astrophysics Data System (ADS)

Howson, Suzanne E.; Bolhuis, Albert; Brabec, Viktor; Clarkson, Guy J.; Malina, Jaroslav; Rodger, Alison; Scott, Peter

2012-01-01

The helicates—chiral assemblies of two or more metal atoms linked by short or relatively rigid multidentate organic ligands—may be regarded as non-peptide mimetics of α-helices because they are of comparable size and have shown some relevant biological activity. Unfortunately, these beautiful helical compounds have remained difficult to use in the medicinal arena because they contain mixtures of isomers, cannot be optimized for specific purposes, are insoluble, or are too difficult to synthesize. Instead, we have now prepared thermodynamically stable single enantiomers of monometallic units connected by organic linkers. Our highly adaptable self-assembly approach enables the rapid preparation of ranges of water-stable, helicate-like compounds with high stereochemical purity. One such iron(II) ‘flexicate’ system exhibits specific interactions with DNA, promising antimicrobial activity against a Gram-positive bacterium (methicillin-resistant Staphylococcus aureus, MRSA252), but also, unusually, a Gram-negative bacterium (Escherichia coli, MC4100), as well as low toxicity towards a non-mammalian model organism (Caenorhabditis elegans).

Probing RNA tertiary structure: interhelical crosslinking of the hammerhead ribozyme.

PubMed Central

Sigurdsson, S T; Tuschl, T; Eckstein, F

1995-01-01

Distinct structural models for the hammerhead ribozyme derived from single-crystal X-ray diffraction and fluorescence resonance energy transfer (FRET) measurements have been compared. Both models predict the same overall geometry, a wishbone shape with helices II and III nearly colinear and helix I positioned close to helix II. However, the relative orientations of helices I and II are different. To establish whether one of the models represents a kinetically active structure, a new crosslinking procedure was developed in which helices I and II of hammerhead ribozymes were disulfide-crosslinked via the 2' positions of specific sugar residues. Crosslinking residues on helices I and II that are close according to the X-ray structure did not appreciably reduce the catalytic efficiency. In contrast, crosslinking residues closely situated according to the FRET model dramatically reduced the cleavage rate by at least three orders of magnitude. These correlations between catalytic efficiencies and spatial proximities are consistent with the X-ray structure. PMID:7489517

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.

ON THE INJECTION OF HELICITY BY THE SHEARING MOTION OF FLUXES IN RELATION TO FLARES AND CORONAL MASS EJECTIONS

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

Vemareddy, P.; Ambastha, A.; Maurya, R. A.

An investigation of helicity injection by photospheric shear motions is carried out for two active regions (ARs), NOAA 11158 and 11166, using line-of-sight magnetic field observations obtained from the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory. We derived the horizontal velocities in the ARs from the differential affine velocity estimator (DAVE) technique. Persistent strong shear motions at maximum velocities in the range of 0.6-0.9 km s{sup -1} along the magnetic polarity inversion line and outward flows from the peripheral regions of the sunspots were observed in the two ARs. The helicities injected in NOAA 11158 and 11166more » during their six-day evolution period were estimated as 14.16 Multiplication-Sign 10{sup 42} Mx{sup 2} and 9.5 Multiplication-Sign 10{sup 42} Mx{sup 2}, respectively. The estimated injection rates decreased up to 13% by increasing the time interval between the magnetograms from 12 minutes to 36 minutes, and increased up to 9% by decreasing the DAVE window size from 21 Multiplication-Sign 18 to 9 Multiplication-Sign 6 pixel{sup 2}, resulting in 10% variation in the accumulated helicity. In both ARs, the flare-prone regions (R2) had inhomogeneous helicity flux distribution with mixed helicities of both signs and coronal mass ejection (CME) prone regions had almost homogeneous distribution of helicity flux dominated by a single sign. The temporal profiles of helicity injection showed impulsive variations during some flares/CMEs due to negative helicity injection into the dominant region of positive helicity flux. A quantitative analysis reveals a marginally significant association of helicity flux with CMEs but not flares in AR 11158, while for the AR 11166, we find a marginally significant association of helicity flux with flares but not CMEs, providing evidence of the role of helicity injection at localized sites of the events. These short-term variations of helicity flux are further discussed in view of possible flare-related effects. This study suggests that flux motions and spatial distribution of helicity injection are important to understanding the complex nature of the magnetic flux system of the AR, and how it can lead to conditions favorable for eruptive events.« less

Structural Analysis of a β-Helical Protein Motif Stabilized by Targeted Replacements with Conformationally Constrained Amino Acids

PubMed Central

Ballano, Gema; Zanuy, David; Jiménez, Ana I.; Cativiela, Carlos; Nussinov, Ruth; Alemán, Carlos

2009-01-01

Here we study conformational stabilization induced in a β-helical nanostructure by position-specific mutations. The nanostructure is constructed through the self-assembly of the β-helical building block excised from E. coli galactoside acetyltransferase (PDB code 1krr, chain A; residues 131-165). The mutations involve substitutions by cyclic, conformationally constrained amino acids. Specifically, a complete structural analysis of the Pro-Xaa-Val sequence [with Xaa being Gly, Ac3c (1-aminocyclopropane-1-carboxylic acid) and Ac5c (1-aminocyclopentane-1-carboxylic acid)], corresponding to the 148-150 loop region in the wild-type (Gly) and mutated (Ac3c and Ac5c) 1krr, has been performed using Molecular Dynamics simulations and X-ray crystallography. Simulations have been performed for the wild-type and mutants of three different systems, namely the building block, the nanoconstruct and the isolated Pro-Xaa-Val tripeptide. Furthermore, the crystalline structures of five peptides of Pro-Xaa-Val or Xaa-Val sequences have been solved by X-ray diffraction analysis and compared with theoretical predictions. Both the theoretical and crystallographic studies indicate that the Pro-Acnc-Val sequences exhibit a high propensity to adopt turn-like conformations, and this propensity is little affected by the chemical environment. Overall, the results indicate that replacement of Gly149 by Ac3c or Ac5c significantly reduce the conformational flexibility of the target site enhancing the structural specificity of the building block and the nanoconstruct derived from the 1krr β-helical motif. PMID:18811190

High-resolution Observations of Flares in an Arch Filament System

NASA Astrophysics Data System (ADS)

Su, Yingna; Liu, Rui; Li, Shangwei; Cao, Wenda; Ahn, Kwangsu; Ji, Haisheng

2018-03-01

We study five sequential solar flares (SOL2015-08-07) occurring in Active Region 12396 observed with the Goode Solar Telescope (GST) at the Big Bear Solar Observatory, complemented by Interface Region Imaging Spectrograph and SDO observations. The main flaring region is an arch filament system (AFS) consisting of multiple bundles of dark filament threads enclosed by semicircular flare ribbons. We study the magnetic configuration and evolution of the active region by constructing coronal magnetic field models based on SDO/HMI magnetograms using two independent methods, i.e., the nonlinear force-free field (NLFFF) extrapolation and the flux rope insertion method. The models consist of multiple flux ropes with mixed signs of helicity, i.e., positive (negative) in the northern (southern) region, which is consistent with the GST observations of multiple filament bundles. The footprints of quasi-separatrix layers (QSLs) derived from the extrapolated NLFFF compare favorably with the observed flare ribbons. An interesting double-ribbon fine structure located at the east border of the AFS is consistent with the fine structure of the QSL’s footprint. Moreover, magnetic field lines traced along the semicircular footprint of a dome-like QSL surrounding the AFS are connected to the regions of significant helicity and Poynting flux injection. The maps of magnetic twist show that positive twist became dominant as time progressed, which is consistent with the injection of positive helicity before the flares. We hence conclude that these circular shaped flares are caused by 3D magnetic reconnection at the QSLs associated with the AFS possessing mixed signs of helicity.

Helicity statistics in homogeneous and isotropic turbulence and turbulence models

NASA Astrophysics Data System (ADS)

Sahoo, Ganapati; De Pietro, Massimo; Biferale, Luca

2017-02-01

We study the statistical properties of helicity in direct numerical simulations of fully developed homogeneous and isotropic turbulence and in a class of turbulence shell models. We consider correlation functions based on combinations of vorticity and velocity increments that are not invariant under mirror symmetry. We also study the scaling properties of high-order structure functions based on the moments of the velocity increments projected on a subset of modes with either positive or negative helicity (chirality). We show that mirror symmetry is recovered at small scales, i.e., chiral terms are subleading and they are well captured by a dimensional argument plus anomalous corrections. These findings are also supported by a high Reynolds numbers study of helical shell models with the same chiral symmetry of Navier-Stokes equations.

Recognition of DNA bulges by dinuclear iron(II) metallosupramolecular helicates.

PubMed

Malina, Jaroslav; Hannon, Michael J; Brabec, Viktor

2014-02-01

Bulged DNA structures are of general biological significance because of their important roles in a number of biochemical processes. Compounds capable of targeting bulged DNA sequences can be used as probes for studying their role in nucleic acid function, or could even have significant therapeutic potential. The interaction of [Fe(2)L(3)](4+) metallosupramolecular helicates (L = C(25)H(20)N(4)) with DNA duplexes containing bulges has been studied by measurement of the DNA melting temperature and gel electrophoresis. This study was aimed at exploring binding affinities of the helicates for DNA bulges of various sizes and nucleotide sequences. The studies reported herein reveal that both enantiomers of [Fe(2)L(3)](4+) bind to DNA bulges containing at least two unpaired nucleotides. In addition, these helicates show considerably enhanced affinity for duplexes containing unpaired pyrimidines in the bulge and/or pyrimidines flanking the bulge on both sides. We suggest that the bulge creates the structural motif, such as the triangular prismatic pocket formed by the unpaired bulge bases, to accommodate the [Fe(2)L(3)](4+) helicate molecule, and is probably responsible for the affinity for duplexes with a varying number of bulge bases. Our results reveal that DNA bulges represent another example of unusual DNA structures recognized by dinuclear iron(II) ([Fe(2)L(3)](4+)) supramolecular helicates. © 2013 FEBS.

Segregation of helicity in inertial wave packets

NASA Astrophysics Data System (ADS)

Ranjan, A.

2017-03-01

Inertial waves are known to exist in the Earth's rapidly rotating outer core and could be important for the dynamo generation. It is well known that a monochromatic inertial plane wave traveling parallel to the rotation axis (along positive z ) has negative helicity while the wave traveling antiparallel (negative z ) has positive helicity. Such a helicity segregation, north and south of the equator, is necessary for the α2-dynamo model based on inertial waves [Davidson, Geophys. J. Int. 198, 1832 (2014), 10.1093/gji/ggu220] to work. The core is likely to contain a myriad of inertial waves of different wave numbers and frequencies. In this study, we investigate whether this characteristic of helicity segregation also holds for an inertial wave packet comprising waves with the same sign of Cg ,z, the z component of group velocity. We first derive the polarization relations for inertial waves and subsequently derive the resultant helicity in wave packets forming as a result of superposition of two or more waves. We find that the helicity segregation does hold for an inertial wave packet unless the wave numbers of the constituent waves are widely separated. In the latter case, regions of opposite color helicity do appear, but the mean helicity retains the expected sign. An illustration of this observation is provided by (a) calculating the resultant helicity for a wave packet formed by superposition of four upward-propagating inertial waves with different wave vectors and (b) conducting the direct numerical simulation of a Gaussian eddy under rapid rotation. Last, the possible effects of other forces such as the viscous dissipation, the Lorentz force, buoyancy stratification, and nonlinearity on helicity are investigated and discussed. The helical structure of the wave packet is likely to remain unaffected by dissipation or the magnetic field, but can be modified by the presence of linearly stable stratification and nonlinearity.

Extended MHD Modeling of Tearing-Driven Magnetic Relaxation

NASA Astrophysics Data System (ADS)

Sauppe, Joshua

2016-10-01

Driven plasma pinch configurations are characterized by the gradual accumulation and episodic release of free energy in discrete relaxation events. The hallmark of this relaxation in a reversed-field pinch (RFP) plasma is flattening of the parallel current density profile effected by a fluctuation-induced dynamo emf in Ohm's law. Nonlinear two-fluid modeling of macroscopic RFP dynamics has shown appreciable coupling of magnetic relaxation and the evolution of plasma flow. Accurate modeling of RFP dynamics requires the Hall effect in Ohm's law as well as first order ion finite Larmor radius (FLR) effects, represented by the Braginskii ion gyroviscous stress tensor. New results find that the Hall dynamo effect from < J × B > / ne can counter the MHD effect from - < V × B > in some of the relaxation events. The MHD effect dominates these events and relaxes the current profile toward the Taylor state, but the opposition of the two dynamos generates plasma flow in the direction of equilibrium current density, consistent with experimental measurements. Detailed experimental measurements of the MHD and Hall emf terms are compared to these extended MHD predictions. Tracking the evolution of magnetic energy, helicity, and hybrid helicity during relaxation identifies the most important contributions in single-fluid and two-fluid models. Magnetic helicity is well conserved relative to the magnetic energy during relaxation. The hybrid helicity is dominated by magnetic helicity in realistic low-beta pinch conditions and is also well conserved. Differences of less than 1 % between magnetic helicity and hybrid helicity are observed with two-fluid modeling and result from cross helicity evolution through ion FLR effects, which have not been included in contemporary relaxation theories. The kinetic energy driven by relaxation in the computations is dominated by velocity components perpendicular to the magnetic field, an effect that had not been predicted. Work performed at University of Wisconsin-Madison. LA-UR-16-24727.

Comparison of helical and cine acquisitions for 4D-CT imaging with multislice CT.

PubMed

Pan, Tinsu

2005-02-01

We proposed a data sufficiency condition (DSC) for four-dimensional-CT (4D-CT) imaging on a multislice CT scanner, designed a pitch factor for a helical 4D-CT, and compared the acquisition time, slice sensitivity profile (SSP), effective dose, ability to cope with an irregular breathing cycle, and gating technique (retrospective or prospective) of the helical 4D-CT and the cine 4D-CT on the General Electric (GE) LightSpeed RT (4-slice), Plus (4-slice), Ultra (8-slice) and 16 (16-slice) multislice CT scanners. To satisfy the DSC, a helical or cine 4D-CT acquisition has to collect data at each location for the duration of a breathing cycle plus the duration of data acquisition for an image reconstruction. The conditions for the comparison were 20 cm coverage in the cranial-caudal direction, a 4 s breathing cycle, and half-scan reconstruction. We found that the helical 4D-CT has the advantage of a shorter scan time that is 10% shorter than that of the cine 4D-CT, and the disadvantages of 1.8 times broadening of SSP and requires an additional breathing cycle of scanning to ensure an adequate sampling at the start and end locations. The cine 4D-CT has the advantages of maintaining the same SSP as slice collimation (e.g., 8 x 2.5 mm slice collimation generates 2.5 mm SSP in the cine 4D-CT as opposed to 4.5 mm in the helical 4D-CT) and a lower dose by 4% on the 8- and 16-slice systems, and 8% on the 4-slice system. The advantage of faster scanning in the helical 4D-CT will diminish if a repeat scan at the location of a breathing irregularity becomes necessary. The cine 4D-CT performs better than the helical 4D-CT in the repeat scan because it can scan faster and is more dose efficient.

Enhanced conformational sampling using enveloping distribution sampling.

PubMed

Lin, Zhixiong; van Gunsteren, Wilfred F

2013-10-14

To lessen the problem of insufficient conformational sampling in biomolecular simulations is still a major challenge in computational biochemistry. In this article, an application of the method of enveloping distribution sampling (EDS) is proposed that addresses this challenge and its sampling efficiency is demonstrated in simulations of a hexa-β-peptide whose conformational equilibrium encompasses two different helical folds, i.e., a right-handed 2.7(10∕12)-helix and a left-handed 3(14)-helix, separated by a high energy barrier. Standard MD simulations of this peptide using the GROMOS 53A6 force field did not reach convergence of the free enthalpy difference between the two helices even after 500 ns of simulation time. The use of soft-core non-bonded interactions in the centre of the peptide did enhance the number of transitions between the helices, but at the same time led to neglect of relevant helical configurations. In the simulations of a two-state EDS reference Hamiltonian that envelops both the physical peptide and the soft-core peptide, sampling of the conformational space of the physical peptide ensures that physically relevant conformations can be visited, and sampling of the conformational space of the soft-core peptide helps to enhance the transitions between the two helices. The EDS simulations sampled many more transitions between the two helices and showed much faster convergence of the relative free enthalpy of the two helices compared with the standard MD simulations with only a slightly larger computational effort to determine optimized EDS parameters. Combined with various methods to smoothen the potential energy surface, the proposed EDS application will be a powerful technique to enhance the sampling efficiency in biomolecular simulations.

Predicting the helix packing of globular proteins by self-correcting distance geometry.

PubMed

Mumenthaler, C; Braun, W

1995-05-01

A new self-correcting distance geometry method for predicting the three-dimensional structure of small globular proteins was assessed with a test set of 8 helical proteins. With the knowledge of the amino acid sequence and the helical segments, our completely automated method calculated the correct backbone topology of six proteins. The accuracy of the predicted structures ranged from 2.3 A to 3.1 A for the helical segments compared to the experimentally determined structures. For two proteins, the predicted constraints were not restrictive enough to yield a conclusive prediction. The method can be applied to all small globular proteins, provided the secondary structure is known from NMR analysis or can be predicted with high reliability.

Tubular Crystals and Helical Arrays: Structural Determination of HIV-1 Capsid Assemblies Using Iterative Helical Real-Space Reconstruction

PubMed Central

Zhang, Peijun; Meng, Xin; Zhao, Gongpu

2013-01-01

Helical structures are important in many different life forms and are well-suited for structural studies by cryo-EM. A unique feature of helical objects is that a single projection image contains all the views needed to perform a three-dimensional (3D) crystallographic reconstruction. Here, we use HIV-1 capsid assemblies to illustrate the detailed approaches to obtain 3D density maps from helical objects. Mature HIV-1 particles contain a conical- or tubular-shaped capsid that encloses the viral RNA genome and performs essential functions in the virus life cycle. The capsid is composed of capsid protein (CA) oligomers which are helically arranged on the surface. The N-terminal domain (NTD) of CA is connected to its C-terminal domain (CTD) through a flexible hinge. Structural analysis of two- and three-dimensional crystals provided molecular models of the capsid protein (CA) and its oligomer forms. We determined the 3D density map of helically assembled HIV-1 CA hexamers at 16 Å resolution using an iterative helical real-space reconstruction method. Docking of atomic models of CA-NTD and CA-CTD dimer into the electron density map indicated that the CTD dimer interface is retained in the assembled CA. Furthermore, molecular docking revealed an additional, novel CTD trimer interface. PMID:23132072

MHD Simulations of Plasma Dynamics with Non-Axisymmetric Boundaries

NASA Astrophysics Data System (ADS)

Hansen, Chris; Levesque, Jeffrey; Morgan, Kyle; Jarboe, Thomas

2015-11-01

The arbitrary geometry, 3D extended MHD code PSI-TET is applied to linear and non-linear simulations of MCF plasmas with non-axisymmetric boundaries. Progress and results from simulations on two experiments will be presented: 1) Detailed validation studies of the HIT-SI experiment with self-consistent modeling of plasma dynamics in the helicity injectors. Results will be compared to experimental data and NIMROD simulations that model the effect of the helicity injectors through boundary conditions on an axisymmetric domain. 2) Linear studies of HBT-EP with different wall configurations focusing on toroidal asymmetries in the adjustable conducting wall. HBT-EP studies the effect of active/passive stabilization with an adjustable ferritic wall. Results from linear verification and benchmark studies of ideal mode growth with and without toroidal asymmetries will be presented and compared to DCON predictions. Simulations of detailed experimental geometries are enabled by use of the PSI-TET code, which employs a high order finite element method on unstructured tetrahedral grids that are generated directly from CAD models. Further development of PSI-TET will also be presented including work to support resistive wall regions within extended MHD simulations. Work supported by DoE.

A unified convention for biological assemblies with helical symmetry

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

Tsai, Chung-Jung, E-mail: tsaic@mail.nih.gov; Nussinov, Ruth; Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978

A new representation of helical structure by four parameters, [n{sub 1}, n{sub 2}, twist, rise], is able to generate an entire helical construct from asymmetric units, including cases of helical assembly with a seam. Assemblies with helical symmetry can be conveniently formulated in many distinct ways. Here, a new convention is presented which unifies the two most commonly used helical systems for generating helical assemblies from asymmetric units determined by X-ray fibre diffraction and EM imaging. A helical assembly is viewed as being composed of identical repetitive units in a one- or two-dimensional lattice, named 1-D and 2-D helical systems,more » respectively. The unification suggests that a new helical description with only four parameters [n{sub 1}, n{sub 2}, twist, rise], which is called the augmented 1-D helical system, can generate the complete set of helical arrangements, including coverage of helical discontinuities (seams). A unified four-parameter characterization implies similar parameters for similar assemblies, can eliminate errors in reproducing structures of helical assemblies and facilitates the generation of polymorphic ensembles from helical atomic models or EM density maps. Further, guidelines are provided for such a unique description that reflects the structural signature of an assembly, as well as rules for manipulating the helical symmetry presentation.« less

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

Yu, M.; Lombardo, V.; Turrioni, D.

Helical solenoids that provide solenoid, helical dipole and helical gradient field components are designed for a helical cooling channel (HCC) proposed for cooling of muon beams in a muon collider. The high temperature superconductor (HTS), 12 mm wide and 0.1 mm thick YBCO tape, is used as the conductor for the highest-field section of HCC due to certain advantages, such as its electrical and mechanical properties. To study and address the design, and technological and performance issues related to magnets based on YBCO tapes, a short helical solenoid model based on double-pancake coils was designed, fabricated and tested at Fermilab.more » Splicing joints were made with Sn-Pb solder as the power leads and the connection between coils, which is the most critical element in the magnet that can limit the performance significantly. This paper summarizes the test results of YBCO tape and double-pancake coils in liquid nitrogen and liquid helium, and then focuses on the study of YBCO splices, including the soldering temperatures and pressures, and splice bending test.« less

Breast conserving treatment for breast cancer: dosimetric comparison of sequential versus simultaneous integrated photon boost.

PubMed

Van Parijs, Hilde; Reynders, Truus; Heuninckx, Karina; Verellen, Dirk; Storme, Guy; De Ridder, Mark

2014-01-01

Breast conserving surgery followed by whole breast irradiation is widely accepted as standard of care for early breast cancer. Addition of a boost dose to the initial tumor area further reduces local recurrences. We investigated the dosimetric benefits of a simultaneously integrated boost (SIB) compared to a sequential boost to hypofractionate the boost volume, while maintaining normofractionation on the breast. For 10 patients 4 treatment plans were deployed, 1 with a sequential photon boost, and 3 with different SIB techniques: on a conventional linear accelerator, helical TomoTherapy, and static TomoDirect. Dosimetric comparison was performed. PTV-coverage was good in all techniques. Conformity was better with all SIB techniques compared to sequential boost (P = 0.0001). There was less dose spilling to the ipsilateral breast outside the PTVboost (P = 0.04). The dose to the organs at risk (OAR) was not influenced by SIB compared to sequential boost. Helical TomoTherapy showed a higher mean dose to the contralateral breast, but less than 5 Gy for each patient. SIB showed less dose spilling within the breast and equal dose to OAR compared to sequential boost. Both helical TomoTherapy and the conventional technique delivered acceptable dosimetry. SIB seems a safe alternative and can be implemented in clinical routine.

Breast Conserving Treatment for Breast Cancer: Dosimetric Comparison of Sequential versus Simultaneous Integrated Photon Boost

PubMed Central

Reynders, Truus; Heuninckx, Karina; Verellen, Dirk; Storme, Guy; De Ridder, Mark

2014-01-01

Background. Breast conserving surgery followed by whole breast irradiation is widely accepted as standard of care for early breast cancer. Addition of a boost dose to the initial tumor area further reduces local recurrences. We investigated the dosimetric benefits of a simultaneously integrated boost (SIB) compared to a sequential boost to hypofractionate the boost volume, while maintaining normofractionation on the breast. Methods. For 10 patients 4 treatment plans were deployed, 1 with a sequential photon boost, and 3 with different SIB techniques: on a conventional linear accelerator, helical TomoTherapy, and static TomoDirect. Dosimetric comparison was performed. Results. PTV-coverage was good in all techniques. Conformity was better with all SIB techniques compared to sequential boost (P = 0.0001). There was less dose spilling to the ipsilateral breast outside the PTVboost (P = 0.04). The dose to the organs at risk (OAR) was not influenced by SIB compared to sequential boost. Helical TomoTherapy showed a higher mean dose to the contralateral breast, but less than 5 Gy for each patient. Conclusions. SIB showed less dose spilling within the breast and equal dose to OAR compared to sequential boost. Both helical TomoTherapy and the conventional technique delivered acceptable dosimetry. SIB seems a safe alternative and can be implemented in clinical routine. PMID:25162031

[Technique of complex mammary irradiation: Mono-isocentric 3D conformational radiotherapy and helical tomotherapy].

PubMed

Vandendorpe, B; Guilbert, P; Champagne, C; Antoni, T; Nguyen, T D; Gaillot-Petit, N; Servagi Vernat, S

2017-12-01

To evaluate the dosimetric contribution of helical tomotherapy for breast cancers compared with conformal radiotherapy in mono-isocentric technique. For 23 patients, the dosimetric results in mono-isocentric 3D conformational radiotherapy did not satisfy the constraints either of target volumes nor organs at risk. A prospective dosimetric comparison between mono-isocentric 3D conformational radiotherapy and helical tomotherapy was therefore carried out. The use of helical tomotherapy showed a benefit in these 23 patients, with either an improvement in the conformity index or homogeneity, but with an increase in low doses. Of the 23 patients, two had pectus excavatum, five had past thoracic irradiation and two required bilateral irradiation. The other 14 patients had a combination of morphology and/or indication of lymph node irradiation. For these patients, helical tomotherapy was therefore preferred to mono-isocentric 3D conformational radiotherapy. Tomotherapy appears to provide better homogeneity and tumour coverage. This technique of irradiation may be justified in the case of morphological situations such as pectus exavatum and in complex clinical situations. In other cases, conformal radiotherapy in mono-isocentric technique remains to be favoured. Copyright © 2017 Société française de radiothérapie oncologique (SFRO). Published by Elsevier SAS. All rights reserved.

Transport of Solar Wind Fluctuations: A Two-Component Model

NASA Technical Reports Server (NTRS)

Oughton, S.; Matthaeus, W. H.; Smith, C. W.; Breech, B.; Isenberg, P. A.

2011-01-01

We present a new model for the transport of solar wind fluctuations which treats them as two interacting incompressible components: quasi-two-dimensional turbulence and a wave-like piece. Quantities solved for include the energy, cross helicity, and characteristic transverse length scale of each component, plus the proton temperature. The development of the model is outlined and numerical solutions are compared with spacecraft observations. Compared to previous single-component models, this new model incorporates a more physically realistic treatment of fluctuations induced by pickup ions and yields improved agreement with observed values of the correlation length, while maintaining good observational accord with the energy, cross helicity, and temperature.

Induced liquid-crystalline ordering in solutions of stiff and flexible amphiphilic macromolecules: Effect of mixture composition

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

Glagolev, Mikhail K.; Vasilevskaya, Valentina V., E-mail: vvvas@polly.phys.msu.ru; Khokhlov, Alexei R.

Impact of mixture composition on self-organization in concentrated solutions of stiff helical and flexible macromolecules was studied by means of molecular dynamics simulation. The macromolecules were composed of identical amphiphilic monomer units but a fraction f of macromolecules had stiff helical backbones and the remaining chains were flexible. In poor solvents the compacted flexible macromolecules coexist with bundles or filament clusters from few intertwined stiff helical macromolecules. The increase of relative content f of helical macromolecules leads to increase of the length of helical clusters, to alignment of clusters with each other, and then to liquid-crystalline-like ordering along a singlemore » direction. The formation of filament clusters causes segregation of helical and flexible macromolecules and the alignment of the filaments induces effective liquid-like ordering of flexible macromolecules. A visual analysis and calculation of order parameter relaying the anisotropy of diffraction allow concluding that transition from disordered to liquid-crystalline state proceeds sharply at relatively low content of stiff components.« less

Helicity dynamics in stratified turbulence in the absence of forcing.

PubMed

Rorai, C; Rosenberg, D; Pouquet, A; Mininni, P D

2013-06-01

A numerical study of decaying stably stratified flows is performed. Relatively high stratification (Froude number ≈10(-2)-10(-1)) and moderate Reynolds (Re) numbers (Re≈ 3-6×10(3)) are considered and a particular emphasis is placed on the role of helicity (velocity-vorticity correlations), which is not an invariant of the nondissipative equations. The problem is tackled by integrating the Boussinesq equations in a periodic cubical domain using different initial conditions: a nonhelical Taylor-Green (TG) flow, a fully helical Beltrami [Arnold-Beltrami-Childress (ABC)] flow, and random flows with a tunable helicity. We show that for stratified ABC flows helicity undergoes a substantially slower decay than for unstratified ABC flows. This fact is likely associated to the combined effect of stratification and large-scale coherent structures. Indeed, when the latter are missing, as in random flows, helicity is rapidly destroyed by the onset of gravitational waves. A type of large-scale dissipative "cyclostrophic" balance can be invoked to explain this behavior. No production of helicity is observed, contrary to the case of rotating and stratified flows. When helicity survives in the system, it strongly affects the temporal energy decay and the energy distribution among Fourier modes. We discover in fact that the decay rate of energy for stratified helical flows is much slower than for stratified nonhelical flows and can be considered with a phenomenological model in a way similar to what is done for unstratified rotating flows. We also show that helicity, when strong, has a measurable effect on the Fourier spectra, in particular at scales larger than the buoyancy scale, for which it displays a rather flat scaling associated with vertical shear, as observed in the planetary boundary layer.

Multipinhole SPECT helical scan parameters and imaging volume

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

Yao, Rutao, E-mail: rutaoyao@buffalo.edu; Deng, Xiao; Wei, Qingyang

Purpose: The authors developed SPECT imaging capability on an animal PET scanner using a multiple-pinhole collimator and step-and-shoot helical data acquisition protocols. The objective of this work was to determine the preferred helical scan parameters, i.e., the angular and axial step sizes, and the imaging volume, that provide optimal imaging performance. Methods: The authors studied nine helical scan protocols formed by permuting three rotational and three axial step sizes. These step sizes were chosen around the reference values analytically calculated from the estimated spatial resolution of the SPECT system and the Nyquist sampling theorem. The nine helical protocols were evaluatedmore » by two figures-of-merit: the sampling completeness percentage (SCP) and the root-mean-square (RMS) resolution. SCP was an analytically calculated numerical index based on projection sampling. RMS resolution was derived from the reconstructed images of a sphere-grid phantom. Results: The RMS resolution results show that (1) the start and end pinhole planes of the helical scheme determine the axial extent of the effective field of view (EFOV), and (2) the diameter of the transverse EFOV is adequately calculated from the geometry of the pinhole opening, since the peripheral region beyond EFOV would introduce projection multiplexing and consequent effects. The RMS resolution results of the nine helical scan schemes show optimal resolution is achieved when the axial step size is the half, and the angular step size is about twice the corresponding values derived from the Nyquist theorem. The SCP results agree in general with that of RMS resolution but are less critical in assessing the effects of helical parameters and EFOV. Conclusions: The authors quantitatively validated the effective FOV of multiple pinhole helical scan protocols and proposed a simple method to calculate optimal helical scan parameters.« less

A morphometric study of the human ear.

PubMed

Alexander, K Skaria; Stott, David J; Sivakumar, Branavan; Kang, Norbert

2011-01-01

We examined variations in the shape of the human ear according to age, sex and ethnic group with particular attention to ear prominence. 420 volunteers were recruited. Measurements included; head height and length, ear height and axis, antihelix taken off angle, earlobe length and width, ear width at the helical root and tragus. Prominence was measured at the helical root and tragus (conchomastoid angle, conchal bowl depth and helical-mastoid distance). Good symmetry was shown for all measurements. Ethnically Indian volunteers had the largest ears (both length and width), followed by Caucasians, and Afro-Caribbeans. This trend was significant in males (p<0.001), but not significant in females (p=0.087). Ears increased in size throughout life. Subjectively, only 2% of volunteers felt their ears were prominent compared to 10% in the opinion of the principal investigator. No objective measurements were identified that accurately predicted subjective perceptions of prominence. We found consistent trends in ear morphology depending on ethnic group, age and sex. Our study was unable to define an objective method for assessing ear prominence. Decisions about what constitutes a prominent ear should be left to personal and aesthetic choice. Copyright © 2010 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

Heat Transfer Enhancement in a Helically Coiled Tube with Al2O3/WATER Nanofluid Under Laminar Flow Condition

NASA Astrophysics Data System (ADS)

Kumar, P. C. Mukesh; Kumar, J.; Suresh, S.; Babu, K. Praveen

2012-10-01

In this experimental investigation, the heat transfer coefficients of a shell and helically coiled tube heat exchanger using Al2O3/water nanofluid under laminar flow condition were studied. The Al2O3 nanoparticles were characterized by X-Ray diffraction (XRD). The Al2O3/water nanofluid at 0.1%, 0.4% and 0.8% particle volume concentration were prepared by using two step method. The prepared nanofluid was characterized by scanning electron microscope (SEM). It is observed that the overall heat transfer coefficient, inner heat transfer coefficient and experimental inner Nusselt number increase while increasing particle volume concentration and increasing inner Dean number. The enhancement of overall heat transfer coefficient was found to be 7%, 16.9% and 24.2% at 0.1%, 0.4% and 0.8% Al2O3/water nanofluid respectively when compared with water. The enhancement of tube side experimental Nusselt number was found to be 17%, 22.9% and 28% at 0.1%, 0.4% and 0.8% particle volume concentration of Al2O3/water nanofluid respectively when compared with water at fixed Dean number. The tests were conducted in the range of 1600 < De < 2700, and 5200 < Re < 8600 under laminar flow condition and counter flow configuration. These enhancements are due to higher thermal conductivity of nanofluid while increasing particle volume concentration and Brownian motion of nanoparticles. It is studied that there is no negative impact on formation of secondary flow and mixing of fluid when nanofluid passes through the helically coiled tube.

Free-fall dynamics of a pair of rigidly linked disks

NASA Astrophysics Data System (ADS)

Kim, Taehyun; Chang, Jaehyeock; Kim, Daegyoum

2018-03-01

We investigate experimentally the free-fall motion of a pair of identical disks rigidly connected to each other. The three-dimensional coordinates of the pair of falling disks were constructed to quantitatively describe its trajectory, and the flow structure formed by the disk pair was identified by using dye visualization. The rigidly linked disk pair exhibits a novel falling pattern that creates a helical path with a conical configuration in which the lower disk rotates in a wider radius than the upper disk with respect to a vertical axis. The helical motion occurs consistently for the range of disk separation examined in this study. The dye visualization reveals that a strong, noticeable helical vortex core is generated from the outer tip of the lower disk during the helical motion. With an increasing length ratio, which is the ratio of the disk separation to the diameter of the disks, the nutation angle and the rate of change in the precession angle that characterize the combined helical and conical kinematics decrease linearly, whereas the pitch of the helical path increases linearly. Although all disk pairs undergo this helical motion, the horizontal-drift patterns of the disk pair depend on the length ratio.

Molecular structure of self-assembled chiral nanoribbons and nanotubules revealed in the hydrated state.

PubMed

Oda, Reiko; Artzner, Franck; Laguerre, Michel; Huc, Ivan

2008-11-05

A detailed molecular organization of racemic 16-2-16 tartrate self-assembled multi-bilayer ribbons in the hydrated state is proposed where 16-2-16 amphiphiles, tartrate ions, and water molecules are all accurately positioned by comparing experimental X-ray powder diffraction and diffraction patterns derived from modeling studies. X-ray diffuse scattering studies show that molecular organization is not fundamentally altered when comparing the flat ribbons of the racemate to chirally twisted or helical ribbons of the pure tartrate enantiomer. Essential features of the three-dimensional molecular organizations of these structures include interdigitation of alkyl chains within each bilayer and well-defined networks of ionic and hydrogen bonds between cations, anions, and water molecules between bilayers. The detailed study of diffraction patterns also indicated that the gemini headgroups are oriented parallel to the long edge of the ribbons. The structure thus possesses a high cohesion and good crystallinity, and for the first time, we could relate the packing of the chiral molecules to the expression of the chirality at a mesoscopic scale. The organization of the ribbons at the molecular level sheds light on a number of their macroscopic features. Among these are the reason why enantiomerically pure 16-2-16 tartrate forms ribbons that consist of exactly two bilayers, and a plausible mechanism by which a chirally twisted or helical shape may emerge from the packing of chiral tartrate ions. Importantly, the distinction between commonly observed helical and twisted morphologies could be related to a subtle symmetry breaking. These results demonstrate that accurately solving the molecular structure of self-assembled soft materials--a process rarely achieved--is within reach, that it is a valid approach to correlate molecular parameters to macroscopic properties, and thus that it offers opportunities to modulate properties through molecular design.

Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix.

PubMed

Zeil, Stephanie; Kovacs, Julio; Wriggers, Willy; He, Jing

2017-01-01

Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably. This method was applied to 79 helices in simulated density maps and six case studies using cryo-EM maps at 6.4-7.7 Å resolution. The arc-length association method is then compared to three existing measures that evaluate the separation of two helical axes: a two-way distance between point sets, the length difference between two axes, and the individual amino acid detection accuracy. The results show that our proposed method sensitively distinguishes lateral and longitudinal discrepancies between the two axes, which makes the method particularly suitable for the systematic investigation of cryo-EM map-model pairs.

Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix

PubMed Central

Zeil, Stephanie; Kovacs, Julio; Wriggers, Willy

2017-01-01

Abstract Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably. This method was applied to 79 helices in simulated density maps and six case studies using cryo-EM maps at 6.4–7.7 Å resolution. The arc-length association method is then compared to three existing measures that evaluate the separation of two helical axes: a two-way distance between point sets, the length difference between two axes, and the individual amino acid detection accuracy. The results show that our proposed method sensitively distinguishes lateral and longitudinal discrepancies between the two axes, which makes the method particularly suitable for the systematic investigation of cryo-EM map–model pairs. PMID:27936925

Helical Poly(5-alkyl-2,3-thiophene)s: Controlled Synthesis and Structure Characterization

DOE PAGES

Zhang, Hong-Hai; Ma, Chuanxu; Bonnesen, Peter V.; ...

2016-07-12

Whereas Poly(3-alkyl-2,5-thiophene)s (P3AT), with many potential applications, have been extensively investigated, their ortho-connected isomers, poly(5-alkyl-2,3-thiophene)s (P5AT), have never been reported because of the difficulty in their syntheses. We herein present the first synthesis of regioregular P5AT via controlled Suzuki cross-coupling polymerization with PEPPSI-IPr as catalyst, affording the polymers with tunable molecular weight, narrow polydispersity (PDI) and well-defined functional end groups at the gram scale. The helical geometry of P5AT was studied by a combination of NMR, small angle x-ray scattering (SAXS) and scanning tunneling microscopy (STM). Particularly, the single polymer chain of poly(5- 2 butyl-2,3-thiophene) (P5BT) on highly oriented pyrolyticmore » graphite (HOPG) substrates with either M or P helical conformation was directly observed by STM. The comparison of UV-vis absorption between poly(5-hexyl-2,3-thiophene) (P5HT) (λ = 345 nm) and poly(3-hexyl-2,5- thiophene) (P3HT) (λ = 450 nm) indicated that the degree of conjugation of the backbone in P5HT is less than in P3HT, which may be a consequence of the helical geometry of the former compared to the more planar geometry of the latter. Moreover, we found that P5HT can emit green fluorescence under UV (λ = 360 nm) irradiation« less

Helically agitated mixing in dry dilute acid pretreatment enhances the bioconversion of corn stover into ethanol

PubMed Central

2014-01-01

Background Dry dilute acid pretreatment at extremely high solids loading of lignocellulose materials demonstrated promising advantages of no waste water generation, less sugar loss, and low steam consumption while maintaining high hydrolysis yield. However, the routine pretreatment reactor without mixing apparatus was found not suitable for dry pretreatment operation because of poor mixing and mass transfer. In this study, helically agitated mixing was introduced into the dry dilute acid pretreatment of corn stover and its effect on pretreatment efficiency, inhibitor generation, sugar production, and bioconversion efficiency through simultaneous saccharification and ethanol fermentation (SSF) were evaluated. Results The overall cellulose conversion taking account of cellulose loss in pretreatment was used to evaluate the efficiency of pretreatment. The two-phase computational fluid dynamics (CFD) model on dry pretreatment was established and applied to analyze the mixing mechanism. The results showed that the pretreatment efficiency was significantly improved and the inhibitor generation was reduced by the helically agitated mixing, compared to the dry pretreatment without mixing: the ethanol titer and yield from cellulose in the SSF reached 56.20 g/L and 69.43% at the 30% solids loading and 15 FPU/DM cellulase dosage, respectively, corresponding to a 26.5% increase in ethanol titer and 17.2% increase in ethanol yield at the same fermentation conditions. Conclusions The advantage of helically agitated mixing may provide a prototype of dry dilute acid pretreatment processing for future commercial-scale production of cellulosic ethanol. PMID:24387051

The PDB database is a rich source of alpha-helical anti-microbial peptides to combat disease causing pathogens.

PubMed

Chakraborty, Sandeep; Phu, My; de Morais, Tâmara Prado; Nascimento, Rafael; Goulart, Luiz Ricardo; Rao, Basuthkar J; Asgeirsson, Bjarni; Dandekar, Abhaya M

2014-01-01

The therapeutic potential of α-helical anti-microbial peptides (AH-AMP) to combat pathogens is fast gaining prominence. Based on recently published open access software for characterizing α-helical peptides (PAGAL), we elucidate a search methodology (SCALPEL) that leverages the massive structural data pre-existing in the PDB database to obtain AH-AMPs belonging to the host proteome. We provide in vitro validation of SCALPEL on plant pathogens ( Xylella fastidiosa, Xanthomonas arboricola and Liberibacter crescens) by identifying AH-AMPs that mirror the function and properties of cecropin B, a well-studied AH-AMP. The identified peptides include a linear AH-AMP present within the existing structure of phosphoenolpyruvate carboxylase (PPC20), and an AH-AMP mimicing the properties of the two α-helices of cecropin B from chitinase (CHITI25). The minimum inhibitory concentration of these peptides are comparable to that of cecropin B, while anionic peptides used as control failed to show any inhibitory effect on these pathogens. Substitute therapies in place of conventional chemotherapies using membrane permeabilizing peptides like these might also prove effective to target cancer cells. The use of native structures from the same organism could possibly ensure that administration of such peptides will be better tolerated and not elicit an adverse immune response. We suggest a similar approach to target Ebola epitopes, enumerated using PAGAL recently, by selecting suitable peptides from the human proteome, especially in wake of recent reports of cationic amphiphiles inhibiting virus entry and infection.

Role of molecular architecture on the relative efficacy of aurein 2.5 and modelin 5.

PubMed

Dennison, Sarah R; Morton, Leslie H G; Phoenix, David A

2012-09-01

In order to gain an insight into the mechanism of antimicrobial peptide action, aurein 2.5 and modelin-5 were studied. When tested against Staphylococcus aureus, aurein 2.5 showed approximately 5-fold greater efficacy even though the higher net positive charge and higher helix stability shown by modelin-5 would have predicated modelin-5 to be the more effective antimicrobial. However, in the presence of S. aureus membrane mimics, aurein 2.5 showed greater helical content (75% helical) relative to modelin-5 (51% helical) indicative of increase in membrane association. This was supported by monolayer data showing that aurein 2.5 (6.6mNm(-1)) generated greater pressure changes than modelin-5 (5.3mNm(-1)). Peptide monolayers indicted that modelin-5 formed a helix horizontal to the plane of an asymmetric interface which would be supported by the even distribution of charge and hydrophobicity along the helical long axis and facilitate lysis by non-specific membrane binding. In contrast, a groove structure observed on the surface of aurein 2.5 was predicted to be the cause of enhanced lipid binding (K(d)=75μM) relative to modelin-5 (K(d)=118μM) and the balance of hydrophobicity along the aurein 2.5 long axis supported deep penetration into the membrane in a tilt formation. This oblique orientation generates greater lytic efficacy in high anionic lipid (71%) compared to modelin-5 (32%). Copyright © 2012 Elsevier B.V. All rights reserved.

The Writhe of Helical Structures in the Solar Corona

NASA Technical Reports Server (NTRS)

Toeroek, T.; Berger, M. A.; Kliem, B.

2010-01-01

Context. Helicity is a fundamental property of magnetic fields, conserved in ideal MHD. In flux rope topology, it consists of twist and writhe helicity. Despite the common occurrence of helical structures in the solar atmosphere, little is known about how their shape relates to the writhe, which fraction of helicity is contained in writhe, and how much helicity is exchanged between twist and writhe when they erupt. Aims. Here we perform a quantitative investigation of these questions relevant for coronal flux ropes. Methods. The decomposition of the writhe of a curve into local and nonlocal components greatly facilitates its computation. We use it to study the relation between writhe and projected S shape of helical curves and to measure writhe and twist in numerical simulations of flux rope instabilities. The results are discussed with regard to filament eruptions and coronal mass ejections (CMEs). Results. (1) We demonstrate that the relation between writhe and projected S shape is not unique in principle, but that the ambiguity does not affect low-lying structures, thus supporting the established empirical rule which associates stable forward (reverse) S shaped structures low in the corona with positive (negative) helicity. (2) Kink-unstable erupting flux ropes are found to transform a far smaller fraction of their twist helicity into writhe helicity than often assumed. (3) Confined flux rope eruptions tend to show stronger writhe at low heights than ejective eruptions (CMEs). This argues against suggestions that the writhing facilitates the rise of the rope through the overlying field. (4) Erupting filaments which are S shaped already before the eruption and keep the sign of their axis writhe (which is expected if field of one chirality dominates the source volume of the eruption), must reverse their S shape in the course of the rise. Implications for the occurrence of the helical kink instability in such events are discussed.

Fast Magnetic Micropropellers with Random Shapes

PubMed Central

2015-01-01

Studying propulsion mechanisms in low Reynolds number fluid has implications for many fields, ranging from the biology of motile microorganisms and the physics of active matter to micromixing in catalysis and micro- and nanorobotics. The propulsion of magnetic micropropellers can be characterized by a dimensionless speed, which solely depends on the propeller geometry for a given axis of rotation. However, this dependence has so far been only investigated for helical propeller shapes, which were assumed to be optimal. In order to explore a larger variety of shapes, we experimentally studied the propulsion properties of randomly shaped magnetic micropropellers. Surprisingly, we found that their dimensionless speeds are high on average, comparable to previously reported nanofabricated helical micropropellers. The highest dimensionless speed we observed is higher than that of any previously reported propeller moving in a low Reynolds number fluid, proving that physical random shape generation can be a viable optimization strategy. PMID:26383225

EVOLUTION OF SPINNING AND BRAIDING HELICITY FLUXES IN SOLAR ACTIVE REGION NOAA 10930

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

Ravindra, B.; Yoshimura, Keiji; Dasso, Sergio, E-mail: ravindra@iiap.res.in, E-mail: yosimura@solar.physics.montana.edu, E-mail: dasso@df.uba.ar

2011-12-10

The line-of-sight magnetograms from Solar Optical Telescope Narrowband Filter Imager observations of NOAA Active Region 10930 have been used to study the evolution of spinning and braiding helicities over a period of five days starting from 2006 December 9. The north (N) polarity sunspot was the follower and the south (S) polarity sunspot was the leader. The N-polarity sunspot in the active region was rotating in the counterclockwise direction. The rate of rotation was small during the first two days of observations and it increased up to 8 Degree-Sign hr{sup -1} on the third day of the observations. On themore » fourth and fifth days it remained at 4 Degree-Sign hr{sup -1} with small undulations in its magnitude. The sunspot rotated about 260 Degree-Sign in the last three days. The S-polarity sunspot did not complete more than 20 Degree-Sign in five days. However, it changed its direction of rotation five times over a period of five days and injected both the positive and negative type of spin helicity fluxes into the corona. Through the five days, both the positive and negative sunspot regions injected equal amounts of spin helicity. The total injected helicity is predominantly negative in sign. However, the sign of the spin and braiding helicity fluxes computed over all the regions were reversed from negative to positive five times during the five-day period of observations. The reversal in spinning helicity flux was found before the onset of the X3.4-class flare, too. Though, the rotating sunspot has been observed in this active region, the braiding helicity has contributed more to the total accumulated helicity than the spinning helicity. The accumulated helicity is in excess of -7 Multiplication-Sign 10{sup 43} Mx{sup 2} over a period of five days. Before the X3.4-class flare that occurred on 2006 December 13, the rotation speed and spin helicity flux increased in the S-polarity sunspot. Before the flare, the total injected helicity was larger than -6 Multiplication-Sign 10{sup 43} Mx{sup 2}. The observed reversal in the sign of spinning and braiding helicity fluxes could be the signature of the emergence of a twisted flux tube, which acquires the writhe of an opposite sign. The magnetic cloud associated with the ejected mass has carried about -7 Multiplication-Sign 10{sup 41} Mx{sup 2} of helicity. A time integration of helicity flux of about 1.2 hr integrated backward in time of the observation of the coronal mass ejection is sufficient for this event.« less

The L49F mutation in alpha erythroid spectrin induces local disorder in the tetramer association region: Fluorescence and molecular dynamics studies of free and bound alpha spectrin

PubMed Central

Song, Yuanli; Pipalia, Nina H; Fung, L W-M

2009-01-01

The bundling of the N-terminal, partial domain helix (Helix C′) of human erythroid α-spectrin (αI) with the C-terminal, partial domain helices (Helices A′ and B′) of erythroid β-spectrin (βI) to give a spectrin pseudo structural domain (triple helical bundle A′B′C′) has long been recognized as a crucial step in forming functional spectrin tetramers in erythrocytes. We have used apparent polarity and Stern–Volmer quenching constants of Helix C′ of αI bound to Helices A′ and B′ of βI, along with previous NMR and EPR results, to propose a model for the triple helical bundle. This model was used as the input structure for molecular dynamics simulations for both wild type (WT) and αI mutant L49F. The simulation output structures show a stable helical bundle for WT, but not for L49F. In WT, four critical interactions were identified: two hydrophobic clusters and two salt bridges. However, in L49F, the region downstream of Helix C′ was unable to assume a helical conformation and one critical hydrophobic cluster was disrupted. Other molecular interactions critical to the WT helical bundle were also weakened in L49F, possibly leading to the lower tetramer levels observed in patients with this mutation-induced blood disorder. PMID:19593814

Results of auricular helical rim reconstruction with post-auricular tube flap.

PubMed

Iljin, Aleksandra; Lewandowicz, Edward; Antoszewski, Bogusław; Zieliński, Tomasz

2016-01-01

The aim of the study was to present our experience with post-auricular tube flap (ptf) and clinical evaluation of the results following auricular helical rim reconstruction with this technique in patients after trauma. We analyzed the results in 12 patients who underwent three-staged auricular helical rim reconstruction with ptf following trauma in the Department of Plastic, Reconstructive and Aesthetic Surgery between 2005-2014. The patients were followed-up for at least 1 year. We evaluated early and long-term results after surgery including plastic surgeon's and patient's opinion. Postoperative results were satisfactory (very good) in 10 cases, both in the opinion of the plastic surgeon and patients. Transient venous congestion of the helix occurred in two cases (16.6%). This complication did not have any influence on estimation of the results after surgery. Delayed wound healing in the poles of the reconstructed helical edge, as well as non-aesthetic helical scars with imperfections of helical rim, were seen in another two patients (16.6%). 1. Post-auricular tube flap reconstructions after helical rim trauma allowed for complete restoration of contour, size and orientation of the helix and the whole operated ear, which confirms the efficiency of the applied technique. 2. Reconstructive surgery with post-auricular tube flap in patients with auricular helical rim defects contributed to postoperative satisfaction in both patients and doctors' estimations.

HELICITY CONSERVATION IN NONLINEAR MEAN-FIELD SOLAR DYNAMO

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

Pipin, V. V.; Sokoloff, D. D.; Zhang, H.

It is believed that magnetic helicity conservation is an important constraint on large-scale astrophysical dynamos. In this paper, we study a mean-field solar dynamo model that employs two different formulations of the magnetic helicity conservation. In the first approach, the evolution of the averaged small-scale magnetic helicity is largely determined by the local induction effects due to the large-scale magnetic field, turbulent motions, and the turbulent diffusive loss of helicity. In this case, the dynamo model shows that the typical strength of the large-scale magnetic field generated by the dynamo is much smaller than the equipartition value for the magneticmore » Reynolds number 10{sup 6}. This is the so-called catastrophic quenching (CQ) phenomenon. In the literature, this is considered to be typical for various kinds of solar dynamo models, including the distributed-type and the Babcock-Leighton-type dynamos. The problem can be resolved by the second formulation, which is derived from the integral conservation of the total magnetic helicity. In this case, the dynamo model shows that magnetic helicity propagates with the dynamo wave from the bottom of the convection zone to the surface. This prevents CQ because of the local balance between the large-scale and small-scale magnetic helicities. Thus, the solar dynamo can operate in a wide range of magnetic Reynolds numbers up to 10{sup 6}.« less

Shear-induced conformational ordering, relaxation, and crystallization of isotactic polypropylene.

PubMed

An, Haining; Li, Xiangyang; Geng, Yong; Wang, Yunlong; Wang, Xiao; Li, Liangbin; Li, Zhongming; Yang, Chuanlu

2008-10-02

The shear-induced coil-helix transition of isotactic polypropylene (iPP) has been studied with time-resolved Fourier transform infrared spectroscopy at various temperatures. The effects of temperature, shear rate, and strain on the coil-helix transition were studied systematically. The induced conformational order increases with the shear rate and strain. A threshold of shear strain is required to induce conformational ordering. High temperature reduces the effect of shear on the conformational order, though a simple correlation was not found. Following the shear-induced conformational ordering, relaxation of helices occurs, which follows the first-order exponential decay at temperatures well above the normal melting point of iPP. The relaxation time versus temperature is fitted with an Arrhenius law, which generates an activation energy of 135 kJ/mol for the helix-coil transition of iPP. At temperatures around the normal melting point, two exponential decays are needed to fit well on the relaxation kinetic of helices. This suggests that two different states of helices are induced by shear: (i) isolated single helices far away from each other without interactions, which have a fast relaxation kinetic; (ii) aggregations of helices or helical bundles with strong interactions among each other, which have a much slower relaxation process. The helical bundles are assumed to be the precursors of nuclei for crystallization. The different helix concentrations and distributions are the origin of the three different processes of crystallization after shear. The correlation between the shear-induced conformational order and crystallization is discussed.

Magnetic chaos healing in the helical reversed-field pinch: indications from the volume-preserving field line tracing code NEMATO

NASA Astrophysics Data System (ADS)

Bonfiglio, D.; Veranda, M.; Cappello, S.; Chacón, L.; Spizzo, G.

2010-11-01

The emergence of a self-organized reversed-field pinch (RFP) helical regime, first shown by 3D MHD numerical simulations, has been highlighted in the RFX-mod experiment at high current operation (IP above 1 MA). In fact, a quasi-stationary helical configuration spontaneously appears, characterized by strong internal electron transport barriers. In such regime electron temperature and density become, to a very good approximation, functions of the helical flux coordinate related to the dominant helical magnetic component. In addition, this regime is diagnosed to be associated with the topological transition to a single-helical-axis (SHAx) state, achieved after the expulsion of the separatrix of the dominant mode's magnetic island. The SHAx state is theoretically predicted to be resilient to the magnetic chaos induced by secondary modes. In this paper, we present initial results of the volume-preserving field line tracing code NEMATO [Finn J M and Chacón L 2005 Phys. Plasmas 12 054503] applied to study the magnetic topology resulting from 3D MHD simulations of the RFP. First, a successful 2D verification test of the code is shown, then, initial application to a systematic study of chaos healing in the helical RFP is discussed. The separatrix disappearance is confirmed to play an essential role for chaos healing. The triggering effect of a reversed magnetic shear for the formation of ordered surfaces within magnetic chaos is also diagnosed.

Magnetic chaos healing in hte helical reversed-field pinch: indications from the volume-preserving field line tracing code NEMATO

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

Bonfiglio, Daniele; Veranda, M.; Cappello, Susanna

2010-01-01

The emergence of a self-organized reversed-field pinch (RFP) helical regime, first shown by 3D MHD numerical simulations, has been highlighted in the RFX-mod experiment at high current operation (IP above 1 MA). In fact, a quasi-stationary helical configuration spontaneously appears, characterized by strong internal electron transport barriers. In such regime electron temperature and density become, to a very good approximation, functions of the helical flux coordinate related to the dominant helical magnetic component. In addition, this regime is diagnosed to be associated with the topological transition to a single-helical-axis (SHAx) state, achieved after the expulsion of the separatrix of themore » dominant mode's magnetic island. The SHAx state is theoretically predicted to be resilient to the magnetic chaos induced by secondary modes. In this paper, we present initial results of the volume-preserving field line tracing code nemato [Finn J M and Chacon L 2005 Phys. Plasmas 12 054503] applied to study the magnetic topology resulting from 3D MHD simulations of the RFP. First, a successful 2D verification test of the code is shown, then, initial application to a systematic study of chaos healing in the helical RFP is discussed. The separatrix disappearance is confirmed to play an essential role for chaos healing. The triggering effect of a reversed magnetic shear for the formation of ordered surfaces within magnetic chaos is also diagnosed.« less

AFM Studies of Salt Concentration Effects on the (110) Surface Structure of Tetragonal Lysozyme Crystals

NASA Technical Reports Server (NTRS)

Pusey, Marc Lee; Gorti, Sridhar; Forsythe, Elizabeth; Konnert, John

2002-01-01

Previous high resolution AFM studies of the (110) surface of tetragonal chicken egg white lysozyme crystals had shown that only one of two possible molecular surfaces is present, those constituting the completed 43 helices. These suggested that the crystal growth process was by the solution-phase assembly of the growth units, which then attach to the surface. However, the best fit for the imaged surfaces, vs. those predicted based upon the bulk crystallographic coordinates, were obtained when the packing about the 43 helices was "tightened up", while maintaining the underlying crystallographic unit cell spacing. This results in a widening of the gap between adjacent helices, and the top- most layer(s) may no longer be in contact. We postulated that the tightened packing about the helices is a result of the high salt concentrations in the bulk solution, used to crystallize the protein, driving hydrophobic interactions. Once the crystal surface is sufficiently buried by subsequent growth layers the ratio of salt to protein molecules decreases and the helices relax to their bulk crystallographic coordinates. The crystal surface helix structure is thus a reflection of the solution structure, and the tightness of the packing about the 43 helices would be a function of the bulk salt concentration. AFM images of the (110) surface of tetragonal lysozyme crystals grown under low (2%) and high (5%) NaCl concentrations reveal differences in the packing about the 43 helices consistent with the above proposal.

Studies of the stability of water-soluble polypeptoid helices and investigation of synthetic, biomimetic substrates for the development of a thermally triggered, enzymatically crosslinked hydrogel for biomedical applications

NASA Astrophysics Data System (ADS)

Sanborn, Tracy Joella

Due to the unique 3D structures of proteins, these biopolymers are able to perform a myriad of vital functions and activities in vivo. Peptidomimetic oligomers are being synthesized to mimic the structure and function of natural peptides. We have examined the stability of secondary structure of a poly-N-substituted glycine (peptoid) and developed synthetic substrates for transglutaminase enzymes. We synthesized an amphipathic, helical, 36 residue peptoid to study the stability of peptoid secondary structure using circular dichroism. We saw no significant dependence of helical structure on concentration, solvent, or temperature. The extraordinary resistance of these peptoid helices to denaturation is consistent with a dominant role, of steric forces in their structural stabilization. The structured polypeptoids studied here have potential as robust mimics of helical polypeptides of therapeutic interest. The ability of transglutaminases to crosslink peptidomimetic substrates was also investigated. There is a medical need for robust, biocompatible hydrogels that can be rapidly crosslinked in situ, for application as surgical adhesives, bone-inductive materials, or for drug delivery. We have taken an enzymatic approach to the creation of a novel gelation system that fits these requirements, utilizing transglutaminase enzymes, thermo-responsive liposomes, and a biomimetic enzyme substrate based on a peptide-polymer conjugate. At room temperature, the hydrogel system is a solution. Upon heating to 37°C, the calcium-loaded liposomes release calcium that activates Factor XIII in the presence of thrombin, producing a gel within 9 minutes. Rheological studies demonstrated that the hydrogel behaves as a robust, elastic solid, while scanning electron microscopy studies revealed that the hydrogel has a very dense morphology overall. We also investigated the ability of transglutaminases to crosslink non-natural, peptoid-based substrates. The activity of five lysine-containing peptoid substrates and two glutamine-containing peptoid substrates with proteinogenic side chains were compared to their peptide analogs. Lysine-containing peptoid substrates were crosslinked by the transglutaminase but at a much lower rate, producing at most 28% of the crosslinked product that its peptide counterpart produced. Of the two glutamine-containing peptoid substrates investigated, one did not show any crosslinked product formation, while the other was insoluble in aqueous solution.

Propulsion and Instability of a Flexible Helical Rod Rotating in a Viscous Fluid

NASA Astrophysics Data System (ADS)

Jawed, M. K.; Khouri, N. K.; Da, F.; Grinspun, E.; Reis, P. M.

2015-10-01

We combine experiments with simulations to investigate the fluid-structure interaction of a flexible helical rod rotating in a viscous fluid, under low Reynolds number conditions. Our analysis takes into account the coupling between the geometrically nonlinear behavior of the elastic rod with a nonlocal hydrodynamic model for the fluid loading. We quantify the resulting propulsive force, as well as the buckling instability of the originally helical filament that occurs above a critical rotation velocity. A scaling analysis is performed to rationalize the onset of this instability. A universal phase diagram is constructed to map out the region of successful propulsion and the corresponding boundary of stability is established. Comparing our results with data for flagellated bacteria suggests that this instability may be exploited in nature for physiological purposes.

Magnetic structure in Mn1 -xCoxGe compounds

NASA Astrophysics Data System (ADS)

Altynbaev, E.; Siegfried, S.-A.; Strauß, P.; Menzel, D.; Heinemann, A.; Fomicheva, L.; Tsvyashchenko, A.; Grigoriev, S.

2018-04-01

The magnetic system of the pseudobinary compound Mn1 -xCoxGe has been studied using small-angle neutron scattering and susceptibility measurements. It is found that Mn1 -xCoxGe orders magnetically at low temperatures in the whole concentration range of x ∈[0 /0.9 ] . Four different states of the magnetic structure have been found at low temperatures: the long-range-ordered (LRO) short-period helical magnetic structure at x

Scaling laws in decaying helical hydromagnetic turbulence

NASA Astrophysics Data System (ADS)

Christensson, M.; Hindmarsh, M.; Brandenburg, A.

2005-07-01

We study the evolution of growth and decay laws for the magnetic field coherence length ξ, energy E_M and magnetic helicity H in freely decaying 3D MHD turbulence. We show that with certain assumptions, self-similarity of the magnetic power spectrum alone implies that ξ σm t1/2. This in turn implies that magnetic helicity decays as Hσm t-2s, where s=(ξ_diff/ξH)2, in terms of ξ_diff, the diffusion length scale, and ξ_H, a length scale defined from the helicity power spectrum. The relative magnetic helicity remains constant, implying that the magnetic energy decays as E_M σm t-1/2-2s. The parameter s is inversely proportional to the magnetic Reynolds number Re_M, which is constant in the self-similar regime.

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.

Enzymatically cross-linked tilapia gelatin hydrogels: physical, chemical, and hybrid networks.

PubMed

Bode, Franziska; da Silva, Marcelo Alves; Drake, Alex F; Ross-Murphy, Simon B; Dreiss, Cécile A

2011-10-10

This Article investigates different types of networks formed from tilapia fish gelatin (10% w/w) in the presence and absence of the enzymatic cross-linker microbial transglutaminase. The influence of the temperature protocol and cross-linker concentration (0-55 U mTGase/g gelatin) was examined in physical, chemical, and hybrid gels, where physical gels arise from the formation of triple helices that act as junction points when the gels are cooled below the gelation point. A combination of rheology and optical rotation was used to study the evolution of the storage modulus (G') over time and the number of triple helices formed for each type of gel. We attempted to separate the final storage modulus of the gels into its chemical and physical contributions to examine the existence or otherwise of synergism between the two types of networks. Our experiments show that the gel characteristics vary widely with the thermal protocol. The final storage modulus in chemical gels increased with enzyme concentration, possibly due to the preferential formation of closed loops at low cross-linker amount. In chemical-physical gels, where the physical network (helices) was formed consecutively to the covalent one, we found that below a critical enzyme concentration the more extensive the chemical network is (as measured by G'), the weaker the final gel is. The storage modulus attributed to the physical network decreased exponentially as a function of G' from the chemical network, but both networks were found to be purely additive. Helices were not thermally stabilized. The simultaneous formation of physical and chemical networks (physical-co-chemical) resulted in G' values higher than the individual networks formed under the same conditions. Two regimes were distinguished: at low enzyme concentration (10-20 U mTGase/g gelatin), the networks were formed in series, but the storage modulus from the chemical network was higher in the presence of helices (compared to pure chemical gels); at higher enzyme concentration (30-40 U mTGase/g gelatin), strong synergistic effects were found as a large part of the covalent network became ineffective upon melting of the helices.

Experiments on helical modes in magnetized thin foil-plasmas

NASA Astrophysics Data System (ADS)

Yager-Elorriaga, David

2017-10-01

This paper gives an in-depth experimental study of helical features on magnetized, ultrathin foil-plasmas driven by the 1-MA linear transformer driver at University of Michigan. Three types of cylindrical liner loads were designed to produce: (a) pure magneto-hydrodynamic (MHD) modes (defined as being void of the acceleration-driven magneto-Rayleigh-Taylor instability, MRT) using a non-imploding geometry, (b) pure kink modes using a non-imploding, kink-seeded geometry, and (c) MRT-MHD coupled modes in an unseeded, imploding geometry. For each configuration, we applied relatively small axial magnetic fields of Bz = 0.2-2.0 T (compared to peak azimuthal fields of 30-40 T). The resulting liner-plasmas and instabilities were imaged using 12-frame laser shadowgraphy and visible self-emission on a fast framing camera. The azimuthal mode number was carefully identified with a tracking algorithm of self-emission minima. Our experiments show that the helical structures are a manifestation of discrete eigenmodes. The pitch angle of the helix is simply m / kR , from implosion to explosion, where m, k, and R are the azimuthal mode number, axial wavenumber, and radius of the helical instability. Thus, the pitch angle increases (decreases) during implosion (explosion) as R becomes smaller (larger). We found that there are one, or at most two, discrete helical modes that arise for magnetized liners, with no apparent threshold on the applied Bz for the appearance of helical modes; increasing the axial magnetic field from zero to 0.5 T changes the relative weight between the m = 0 and m = 1 modes. Further increasing the applied axial magnetic fields yield higher m modes. Finally, the seeded kink instability overwhelms the intrinsic instability modes of the plasma. These results are corroborated with our analytic theory on the effects of radial acceleration on the classical sausage, kink, and higher m modes. Work supported by US DOE award DE-SC0012328, Sandia National Laboratories, and the National Science Foundation. D.Y.E. was supported by NSF fellowship Grant Number DGE 1256260. The fast framing camera was supported by a DURIP, AFOSR Grant FA9550-15-1-0419.

Transition to Turbulence in curved pipe

NASA Astrophysics Data System (ADS)

Hashemi, Amirreza; Loth, Francis

2014-11-01

Studies have shown that transitional turbulence in a curved pipe is delayed significantly compared with straight pipes. These analytical, numerical and experimental studies employed a helical geometry that is infinitely long such that the effect of the inlet and outlet can be neglected. The present study examined transition to turbulence in a finite curved pipe with a straight inlet/outlet and a 180 degrees curved pipe with a constant radius of curvature and diameter (D). We have employed the large scale direct numerical simulation (DNS) by using the spectral element method, nek5000, to simulate the flow field within curved pipe geometry with different curvature radii and Reynolds numbers to determine the point of the transition to turbulence. Long extensions for the inlet (5D) and outlet (20D) were used to diminish the effect of the boundary conditions. Our numerical results for radius of curvatures of 1.5D and 5D show transition turbulence is near Re = 3000. This is delayed compared with a straight pipe (Re = 2200) but still less that observed for helical geometries (Reynolds number less than 5000). Our research aims to describe the critical Reynolds number for transition to turbulence for a finite curved pipe at various curvature radii.

A case study for online plan adaptation using helical tomotherapy

PubMed Central

Neilson, Christopher E.; Yartsev, Slav

2012-01-01

Helical tomotherapy's ability to provide daily megavoltage (MV) computed tomography (CT) images for patient set-up verification allows for the creation of adapted plans. As plans become more complex by introducing sharper dose gradients in an effort to spare healthy tissue, inter-fraction changes of organ position with respect to plan become a limiting factor in the correct dose delivery to the target. Tomotherapy's planned adaptive option provides the possibility to evaluate the dose distribution for each fraction and subsequently adapt the original plan to the current anatomy. In this study, 30 adapted plans were created using new contours based on the daily MVCT studies of a bladder cancer patient with considerable anatomical variations. Dose to the rectum and two planning target volumes (PTVs) were compared between the original plan, the dose that was actually delivered to the patient, and the theoretical dose from the 30 adapted plans. The adaptation simulation displayed a lower dose to 35% and 50% of the rectum compared to no adaptation at all, while maintaining an equivalent dose to the PTVs. Although online adaptation is currently too time-consuming, it has the potential to improve the effectiveness of radiotherapy. PMID:22557799

Optical-vortex pair creation and annihilation and helical astigmatism of a nonplanar ring resonator

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

Heckenberg, N.R.; Vaupel, M.; Malos, J.T.

1996-09-01

The creation and annihilation of pairs of optical vortices have been studied in transitions between patterns produced in a photorefractive oscillator. Smooth metamorphosis between stable patterns occurs through pair creation or annihilation but can be modeled using superposition of modes taking into account lifting of degeneracy of helical modes by helical astigmatism of the resonator. {copyright} {ital 1996 The American Physical Society.}

Helicity of short E-R/K peptides.

PubMed

Sommese, Ruth F; Sivaramakrishnan, Sivaraj; Baldwin, Robert L; Spudich, James A

2010-10-01

Understanding the secondary structure of peptides is important in protein folding, enzyme function, and peptide-based drug design. Previous studies of synthetic Ala-based peptides (>12 a.a.) have demonstrated the role for charged side chain interactions involving Glu/Lys or Glu/Arg spaced three (i, i + 3) or four (i, i + 4) residues apart. The secondary structure of short peptides (<9 a.a.), however, has not been investigated. In this study, the effect of repetitive Glu/Lys or Glu/Arg side chain interactions, giving rise to E-R/K helices, on the helicity of short peptides was examined using circular dichroism. Short E-R/K-based peptides show significant helix content. Peptides containing one or more E-R interactions display greater helicity than those with similar E-K interactions. Significant helicity is achieved in Arg-based E-R/K peptides eight, six, and five amino acids long. In these short peptides, each additional i + 3 and i + 4 salt bridge has substantial contribution to fractional helix content. The E-R/K peptides exhibit a strongly linear melt curve indicative of noncooperative folding. The significant helicity of these short peptides with predictable dependence on number, position, and type of side chain interactions makes them an important consideration in peptide design.

Does Hooke's law work in helical nanosprings?

PubMed

Ben, Sudong; Zhao, Junhua; Rabczuk, Timon

2015-08-28

Hooke's law is a principle of physics that states that the force needed to extend a spring by some distance is proportional to that distance. The law is always valid for an initial portion of the elastic range for nearly all helical macrosprings. Here we report the sharp nonlinear force-displacement relation of tightly wound helical carbon nanotubes at even small displacement via a molecular mechanics model. We demonstrate that the van der Waals (vdW) interaction between the intertube walls dominates the nonlinear relation based on our analytical expressions. This study provides physical insights into the origin of huge nonlinearity of the helical nanosprings.

STABLE CONIC-HELICAL ORBITS OF PLANETS AROUND BINARY STARS: ANALYTICAL RESULTS

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

Oks, E.

2015-05-10

Studies of planets in binary star systems are especially important because it was estimated that about half of binary stars are capable of supporting habitable terrestrial planets within stable orbital ranges. One-planet binary star systems (OBSS) have a limited analogy to objects studied in atomic/molecular physics: one-electron Rydberg quasimolecules (ORQ). Specifically, ORQ, consisting of two fully stripped ions of the nuclear charges Z and Z′ plus one highly excited electron, are encountered in various plasmas containing more than one kind of ion. Classical analytical studies of ORQ resulted in the discovery of classical stable electronic orbits with the shape ofmore » a helix on the surface of a cone. In the present paper we show that despite several important distinctions between OBSS and ORQ, it is possible for OBSS to have stable planetary orbits in the shape of a helix on a conical surface, whose axis of symmetry coincides with the interstellar axis; the stability is not affected by the rotation of the stars. Further, we demonstrate that the eccentricity of the stars’ orbits does not affect the stability of the helical planetary motion if the center of symmetry of the helix is relatively close to the star of the larger mass. We also show that if the center of symmetry of the conic-helical planetary orbit is relatively close to the star of the smaller mass, a sufficiently large eccentricity of stars’ orbits can switch the planetary motion to the unstable mode and the planet would escape the system. We demonstrate that such planets are transitable for the overwhelming majority of inclinations of plane of the stars’ orbits (i.e., the projections of the planet and the adjacent start on the plane of the sky coincide once in a while). This means that conic-helical planetary orbits at binary stars can be detected photometrically. We consider, as an example, Kepler-16 binary stars to provide illustrative numerical data on the possible parameters and the stability of the conic-helical planetary orbits, as well as on the transitability. Then for the general case, we also show that the power of the gravitational radiation due to this planet can be comparable or even exceed the power of the gravitational radiation due to the stars in the binary. This means that in the future, with a progress of gravitational wave detectors, the presence of a planet in a conic-helical orbit could be revealed by the noticeably enhanced gravitational radiation from the binary star system.« less

Study of goldfish (Carassius auratus) growth hormone structure-function relationship by domain swapping.

PubMed

Chan, Y H; Cheng, C H K; Chan, K M

2007-03-01

Using goldfish as a model, the structure-function relationship of goldfish growth hormone was studied using the strategy of homologous domain swapping. Chimeric mutants were constructed by exchanging homologous regions between goldfish growth hormone (gfGH II) and goldfish prolactin (gfPRL) with their cloned complementary DNAs. Six mutants, with their domain-swapped, were generated to have different combinations of three target regions, including the helix a, helix d and the large section in between these helices (possess the helices b, c and other random coiled regions). After expression in E. coli and refolding, these mutants were characterized by using competitive receptor binding assay (RRA) and growth hormone responding promoter activation assay. The different activity profiles of mutants in Spi 2.1 gene promoter assays from that in RRA shows that, for gfGH, receptor binding dose not confer receptor signal activations. When either helices a or d of gfGH was maintained with other helices replaced by their gfPRL counterparts, both receptor binding and hence gene activation activities are reduced. In mutants with helices b and c in gfGH maintained, containing the gfGH middle section, and helices a and d swapped with gfPRL, the had reduced RRA activities but the promoter activation activities retained. In conclusion, as in the case of human GH, the gfGH molecule possesses two functional sites: one of them is composed of discontinuous epitopes located on the target regions of this study and is for receptor binding; another site is located on the middle section of the molecule that helices a and d are not involved, and it is for activation of GH receptor and intracellular signals.

A Sidekick for Membrane Simulations: Automated Ensemble Molecular Dynamics Simulations of Transmembrane Helices

PubMed Central

Hall, Benjamin A; Halim, Khairul Abd; Buyan, Amanda; Emmanouil, Beatrice; Sansom, Mark S P

2016-01-01

The interactions of transmembrane (TM) α-helices with the phospholipid membrane and with one another are central to understanding the structure and stability of integral membrane proteins. These interactions may be analysed via coarse-grained molecular dynamics (CGMD) simulations. To obtain statistically meaningful analysis of TM helix interactions, large (N ca. 100) ensembles of CGMD simulations are needed. To facilitate the running and analysis of such ensembles of simulations we have developed Sidekick, an automated pipeline software for performing high throughput CGMD simulations of α-helical peptides in lipid bilayer membranes. Through an end-to-end approach, which takes as input a helix sequence and outputs analytical metrics derived from CGMD simulations, we are able to predict the orientation and likelihood of insertion into a lipid bilayer of a given helix of family of helix sequences. We illustrate this software via analysis of insertion into a membrane of short hydrophobic TM helices containing a single cationic arginine residue positioned at different positions along the length of the helix. From analysis of these ensembles of simulations we estimate apparent energy barriers to insertion which are comparable to experimentally determined values. In a second application we use CGMD simulations to examine self-assembly of dimers of TM helices from the ErbB1 receptor tyrosine kinase, and analyse the numbers of simulation repeats necessary to obtain convergence of simple descriptors of the mode of packing of the two helices within a dimer. Our approach offers proof-of-principle platform for the further employment of automation in large ensemble CGMD simulations of membrane proteins. PMID:26580541

Sidekick for Membrane Simulations: Automated Ensemble Molecular Dynamics Simulations of Transmembrane Helices.

PubMed

Hall, Benjamin A; Halim, Khairul Bariyyah Abd; Buyan, Amanda; Emmanouil, Beatrice; Sansom, Mark S P

2014-05-13

The interactions of transmembrane (TM) α-helices with the phospholipid membrane and with one another are central to understanding the structure and stability of integral membrane proteins. These interactions may be analyzed via coarse grained molecular dynamics (CGMD) simulations. To obtain statistically meaningful analysis of TM helix interactions, large (N ca. 100) ensembles of CGMD simulations are needed. To facilitate the running and analysis of such ensembles of simulations, we have developed Sidekick, an automated pipeline software for performing high throughput CGMD simulations of α-helical peptides in lipid bilayer membranes. Through an end-to-end approach, which takes as input a helix sequence and outputs analytical metrics derived from CGMD simulations, we are able to predict the orientation and likelihood of insertion into a lipid bilayer of a given helix of a family of helix sequences. We illustrate this software via analyses of insertion into a membrane of short hydrophobic TM helices containing a single cationic arginine residue positioned at different positions along the length of the helix. From analyses of these ensembles of simulations, we estimate apparent energy barriers to insertion which are comparable to experimentally determined values. In a second application, we use CGMD simulations to examine the self-assembly of dimers of TM helices from the ErbB1 receptor tyrosine kinase and analyze the numbers of simulation repeats necessary to obtain convergence of simple descriptors of the mode of packing of the two helices within a dimer. Our approach offers a proof-of-principle platform for the further employment of automation in large ensemble CGMD simulations of membrane proteins.

Non-Native α-Helices in the Initial Folding Intermediate Facilitate the Ordered Assembly of the β-Barrel in β-Lactoglobulin.

PubMed

Sakurai, Kazumasa; Yagi, Masanori; Konuma, Tsuyoshi; Takahashi, Satoshi; Nishimura, Chiaki; Goto, Yuji

2017-09-12

The roles of non-native α-helices frequently observed in the initial folding stage of β-sheet proteins have been examined for many years. We herein investigated the residue-level structures of several mutants of bovine β-lactoglobulin (βLG) in quenched-flow pH-pulse labeling experiments. βLG assumes a collapsed intermediate with a non-native α-helical structure (I 0 ) in the early stage of folding, although its native form is predominantly composed of β-structures. The protection profile in I 0 of pseudo-wild type (WT*) βLG was found to deviate from the pattern of the "average area buried upon folding" (AABUF). In particular, the level of protection at the region of strand A, at which non-native α-helices form in the I 0 state, was significantly low compared to AABUF. G17E, the mutant with an increased helical propensity, showed a similar protection pattern. In contrast, the protection pattern for I 0 of E44L, the mutant with an increased β-sheet propensity, was distinct from that of WT* and resembled the AABUF pattern. Transverse relaxation measurements demonstrated that the positions of the residual structures in the unfolded states of these mutants were consistent with those of the protected residues in the respective I 0 states. On the basis of the slower conversion of I 0 to the native state for E44L to that for WT*, non-native α-helices facilitate the ordered assembly of the β-barrel by preventing interactions that trap folding.

Solitons in a nonlinear model of spin transport in helical molecules

NASA Astrophysics Data System (ADS)

Albares, P.; Díaz, E.; Cerveró, Jose M.; Domínguez-Adame, F.; Diez, E.; Estévez, P. G.

2018-02-01

We study an effective integrable nonlinear model describing an electron moving along the axis of a deformable helical molecule. The helical conformation of dipoles in the molecular backbone induces an unconventional Rashba-like interaction that couples the electron spin with its linear momentum. In addition, a focusing nonlinearity arises from the electron-lattice interaction, enabling the formation of a variety of stable solitons such as bright solitons, breathers, and rogue waves. A thorough study of the soliton solutions for both focusing and defocusing nonlinear interaction is presented and discussed.

Conformational phases of membrane bound cytoskeletal filaments

NASA Astrophysics Data System (ADS)

Quint, David A.; Grason, Gregory; Gopinathan, Ajay

2013-03-01

Membrane bound cytoskeletal filaments found in living cells are employed to carry out many types of activities including cellular division, rigidity and transport. When these biopolymers are bound to a membrane surface they may take on highly non-trivial conformations as compared to when they are not bound. This leads to the natural question; What are the important interactions which drive these polymers to particular conformations when they are bound to a surface? Assuming that there are binding domains along the polymer which follow a periodic helical structure set by the natural monomeric handedness, these bound conformations must arise from the interplay of the intrinsic monomeric helicity and membrane binding. To probe this question, we study a continuous model of an elastic filament with intrinsic helicity and map out the conformational phases of this filament for various mechanical and structural parameters in our model, such as elastic stiffness and intrinsic twist of the filament. Our model allows us to gain insight into the possible mechanisms which drive real biopolymers such as actin and tubulin in eukaryotes and their prokaryotic cousins MreB and FtsZ to take on their functional conformations within living cells.

Numerical Assessment of Novel Helical/Spiral Grafts with Improved Hemodynamics for Distal Graft Anastomoses

PubMed Central

Kabinejadian, Foad; McElroy, Michael; Ruiz-Soler, Andres; Leo, Hwa Liang; Slevin, Mark A.; Badimon, Lina

2016-01-01

In the present work, numerical simulations were conducted for a typical end-to-side distal graft anastomosis to assess the effects of inducing secondary flow, which is believed to remove unfavourable flow environment. Simulations were carried out for four models, generated based on two main features of 'out-of-plane helicity' and 'spiral ridge' in the grafts as well as their combination. Following a qualitative comparison against in vitro data, various mean flow and hemodynamic parameters were compared and the results showed that helicity is significantly more effective in inducing swirling flow in comparison to a spiral ridge, while their combination could be even more effective. In addition, the induced swirling flow was generally found to be increasing the wall shear stress and reducing the flow stagnation and particle residence time within the anastomotic region and the host artery, which may be beneficial to the graft longevity and patency rates. Finally, a parametric study on the spiral ridge geometrical features was conducted, which showed that the ridge height and the number of spiral ridges have significant effects on inducing swirling flow, and revealed the potential of improving the efficiency of such designs. PMID:27861485

Non-Solenoidal Startup Research Directions on the Pegasus Toroidal Experiment

NASA Astrophysics Data System (ADS)

Fonck, R. J.; Bongard, M. W.; Lewicki, B. T.; Reusch, J. A.; Winz, G. R.

2017-10-01

The Pegasus research program has been focused on developing a physical understanding and predictive models for non-solenoidal tokamak plasma startup using Local Helicity Injection (LHI). LHI employs strong localized electron currents injected along magnetic field lines in the plasma edge that relax through magnetic turbulence to form a tokamak-like plasma. Pending approval, the Pegasus program will address a broader, more comprehensive examination of non-solenoidal tokamak startup techniques. New capabilities may include: increasing the toroidal field to 0.6 T to support critical scaling tests to near-NSTX-U field levels; deploying internal plasma diagnostics; installing a coaxial helicity injection (CHI) capability in the upper divertor region; and deploying a modest (200-400 kW) electron cyclotron RF capability. These efforts will address scaling of relevant physics to higher BT, separate and comparative studies of helicity injection techniques, efficiency of handoff to consequent current sustainment techniques, and the use of ECH to synergistically improve the target plasma for consequent bootstrap and neutral beam current drive sustainment. This has an ultimate goal of validating techniques to produce a 1 MA target plasma in NSTX-U and beyond. Work supported by US DOE Grant DE-FG02-96ER54375.

Theory of formation of helical structures in a perfectly conducting, premagnetized Z-pinch liner

NASA Astrophysics Data System (ADS)

Yu, Edmund; Velikovich, Alexander; Peterson, Kyle

2014-10-01

The magnetized liner inertial fusion (MagLIF) concept uses an azimuthal magnetic field to collapse a thick metallic liner containing preheated fusion fuel. A critical component of the concept is an axial magnetic field, permeating both the fuel and surrounding liner, which reduces the compression necessary to achieve fusion conditions. Recent experiments demonstrate that a liner premagnetized with a 10 T axial field develops helical structures with a pitch significantly larger than an estimate of Bz /Bθ would suggest. The cause of the helical perturbations is still not understood. In this work, we present an analytic, linear theory in which we model the liner as a perfectly conducting metal, and study how bumps and divots on its surface redirect current flow, resulting in perturbations to B as well as j × B . We show that in the presence of axial and azimuthal magnetic field, the theory predicts divots will grow and deform at an angle determined by the magnetic field. We compare theoretical results with three dimensional, resistive MHD simulations. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the National Nuclear Security Administration under DE-AC04-94AL85000.

Probing magnetic helicity with synchrotron radiation and Faraday rotation

NASA Astrophysics Data System (ADS)

Oppermann, N.; Junklewitz, H.; Robbers, G.; Enßlin, T. A.

2011-06-01

We present a first application of the recently proposed LITMUS test for magnetic helicity, as well as a thorough study of its applicability under different circumstances. In order to apply this test to the galactic magnetic field, the newly developed critical filter formalism is used to produce an all-sky map of the Faraday depth. The test does not detect helicity in the galactic magnetic field. To understand the significance of this finding, we made an applicability study, showing that a definite conclusion about the absence of magnetic helicity in the galactic field has not yet been reached. This study is conducted by applying the test to simulated observational data. We consider simulations in a flat sky approximation and all-sky simulations, both with assumptions of constant electron densities and realistic distributions of thermal and cosmic ray electrons. Our results suggest that the LITMUS test does indeed perform very well in cases where constant electron densities can be assumed, both in the flat-sky limit and in the galactic setting. Non-trivial distributions of thermal and cosmic ray electrons, however, may complicate the scenario to the point where helicity in the magnetic field can escape detection.

Reconnection and Associated Flares in Global Relativistic Jets Containing Helical Magnetic Fields with PIC Simulations

NASA Astrophysics Data System (ADS)

Nishikawa, Ken-Ichi; Hartmann, Dieter; Mizuno, Yosuke; Niemiec, Jacek; Dutan, Ioana; Kobzar, Oleh; Gomez, Jose; Meli, Athina; POHL, Martin

2018-01-01

In the study of relativistic jets one of the key open questions is their interaction with theenvironment on the microscopic level. Here, we study the initial evolution of both electron–proton and electron–positron relativistic jets containing helical magnetic fields, focusing on their interaction with an ambient plasma. We have performed simulations of “global” jets containing helical magnetic fields in order to examine how helical magnetic fields affect kinetic instabilities such as the Weibel instability, the kinetic Kelvin-Helmholtz instability (kKHI) and the Mushroom instability (MI) using a larger jet radius. In our initial simulation study these kinetic instabilities are suppressed and new types of instabilities can grow. In the electron-proton jet simulation a recollimation-like instability occurs near the center of jet. In the electron-positron jet simulation mixed kinetic instabilities grow and the jet electrons are accelerated. The evolution of electron-ion jets will be investigated with different mass ratios. Simulations using much larger systems are required in order to thoroughly follow the evolution of global jets containing helical magnetic fields. We will investigate mechanisms of flares possibly due to reconnection.

Deceleration of arginine kinase refolding by induced helical structures.

PubMed

Li, Hai-Long; Zhou, Sheng-Mei; Park, Daeui; Jeong, Hyoung Oh; Chung, Hae Young; Yang, Jun-Mo; Meng, Fan-Guo; Hu, Wei-Jiang

2012-04-01

Arginine kinase (AK) is a key metabolic enzyme for keeping energy balance in invertebrates. Therefore, regulation of the enzymatic activity and the folding studies of AK from the various invertebrates have been the focus of investigation. We studied the effects of helical structures by using hexafluoroisopropanol (HFIP) on AK folding. Folding kinetic studies showed that the folding rates of the urea-denatured AKs were significantly decelerated after being induced in various concentrations of HFIP. AK lost its activity completely at concentrations greater than 60%. The results indicated that the HFIP-induced helical structures in the denatured state play a negative role in protein folding, and the helical structures induced in 5% (v/v) HFIP act as the most effective barrier against AK taking its native structure. The computational docking simulations (binding energies for -2.19 kcal/mol for AutoDock4.2 and -20.47 kcal/mol for Dock6.3) suggested that HFIP interacts with the several important residues that are predicted by both programs. The excessively pre-organized helical structures not only hampered the folding process, but also ultimately brought about changes in the three-dimensional conformation and biological function of AK.

Local conformational dynamics in alpha-helices measured by fast triplet transfer.

PubMed

Fierz, Beat; Reiner, Andreas; Kiefhaber, Thomas

2009-01-27

Coupling fast triplet-triplet energy transfer (TTET) between xanthone and naphthylalanine to the helix-coil equilibrium in alanine-based peptides allowed the observation of local equilibrium fluctuations in alpha-helices on the nanoseconds to microseconds time scale. The experiments revealed faster helix unfolding in the terminal regions compared with the central parts of the helix with time constants varying from 250 ns to 1.4 micros at 5 degrees C. Local helix formation occurs with a time constant of approximately 400 ns, independent of the position in the helix. Comparing the experimental data with simulations using a kinetic Ising model showed that the experimentally observed dynamics can be explained by a 1-dimensional boundary diffusion with position-independent elementary time constants of approximately 50 ns for the addition and of approximately 65 ns for the removal of an alpha-helical segment. The elementary time constant for helix growth agrees well with previously measured time constants for formation of short loops in unfolded polypeptide chains, suggesting that helix elongation is mainly limited by a conformational search.

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

Experimental and density functional theory (DFT) studies on the interactions of Ru(II) polypyridyl complexes with the RAN triplex poly(U)˙poly(A)*poly(U).

PubMed

Zhang, Hong; Liu, Xuewen; He, Xiaojun; Liu, Ying; Tan, Lifeng

2014-11-01

There is renewed interest in investigating triple helices because these novel structures have been implicated as a possible means of controlling cellular processes by endogenous or exogenous mechanisms. Due to the Hoogsteen base pairing, triple helices are, however, thermodynamically less stable than the corresponding duplexes. The poor stability of triple helices limits their practical applications under physiological conditions. In contrast to DNA triple helices, small molecules stabilizing RNA triple helices at present are less well established. Furthermore, most of these studies are limited to organic compounds and, to a far lesser extent, to metal complexes. In this work, two Ru(II) complexes, [Ru(bpy)2(btip)](2+) (Ru1) and [Ru(phen)2(btip)](2+) (Ru2), have been synthesized and characterized. The binding properties of the two metal complexes with the triple RNA poly(U)˙poly(A)*poly(U) were studied by various biophysical and density functional theory methods. The main results obtained here suggest that the slight binding difference in Ru1 and Ru2 may be attributed to the planarity of the intercalative ligand and the LUMO level of Ru(II) complexes. This study further advances our knowledge on the triplex RNA-binding by metal complexes, particularly Ru(II) complexes.

Small-scale anisotropy induced by spectral forcing and by rotation in non-helical and helical turbulence

NASA Astrophysics Data System (ADS)

Vallefuoco, Donato; Naso, Aurore; Godeferd, Fabien S.

2018-02-01

We study the effect of large-scale spectral forcing on the scale-dependent anisotropy of the velocity field in direct numerical simulations of homogeneous turbulence. ABC-type forcing and helical or non-helical Euler-type forcing are considered. We propose a scale-dependent characterisation of anisotropy based on a modal decomposition of the two-point velocity tensor spectrum. This produces direction-dependent spectra of energy, helicity and polarisation. We examine the conditions that allow anisotropy to develop in the small scales due to forcing and we show that the theoretically expected isotropy is not exactly obtained, even in the smallest scales, for ABC and helical Euler forcings. When adding rotation, the anisotropy level in ABC-forced simulations is similar to that of lower Rossby number Euler-forced runs. Moreover, even at low rotation rate, the natural anisotropy induced by the Coriolis force is visible at all scales, and two distinct wavenumber ranges appear from our fine-grained characterisation, not separated by the Zeman scale but by a scale where rotation and dissipation are balanced.

Disentangling the triadic interactions in Navier-Stokes equations.

PubMed

Sahoo, Ganapati; Biferale, Luca

2015-10-01

We study the role of helicity in the dynamics of energy transfer in a modified version of the Navier-Stokes equations with explicit breaking of the mirror symmetry. We select different set of triads participating in the dynamics on the basis of their helicity content. In particular, we remove the negative helically polarized Fourier modes at all wave numbers except for those falling on a localized shell of wave number, |k| ~ k(m). Changing k(m) to be above or below the forcing scale, k(f), we are able to assess the energy transfer of triads belonging to different interaction classes. We observe that when the negative helical modes are present only at a wave number smaller than the forced wave numbers, an inverse energy cascade develops with an accumulation of energy on a stationary helical condensate. Vice versa, when negative helical modes are present only at a wave number larger than the forced wave numbers, a transition from backward to forward energy transfer is observed in the regime when the minority modes become energetic enough.

Fabrication of CA/TPU Helical Nanofibers and its Mechanism Analysis

NASA Astrophysics Data System (ADS)

Wu, Huihui; Zhao, Shihang; Han, Lei

2018-04-01

To explore the mechanism of cellulose acetate (CA)/thermoplastic polyurethane (TPU) on the fabrication of helical nanofibers, a series of experiments were conducted to find the optimum spinning conditions. The experimental results show that the CA (14 wt%, DMAc/acetone, 1/2 volume ratio)/TPU2 (18 wt%, DMAc/acetone, 3/1 volume ratio) system can fabricate helical nanofibers effectively via co-electrospinning. We focus on the interfacial interaction between the polymer components induced by the polymer structure and intrinsic properties, including solution properties, hydrogen bonding, and miscibility behavior of the two solutions. Differential scanning calorimetry (DSC) and Fourier transform infrared spectroscopy (FTIR) are employed to investigate the interfacial interaction between the two phases of the polymer system. The analysis results provide the explanation of the experimental results that the CA/TPU system has the potential for producing helical nanofibers effectively. This study based on the interfacial interaction between polymer components provides an insight into the mechanism of CA/TPU helical fiber formation and introduces a richer choice of materials for the application of helical fibers.

Reduced bispectrum seeded by helical primordial magnetic fields

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

Hortúa, Héctor Javier; Castañeda, Leonardo, E-mail: hjhortuao@unal.edu.co, E-mail: lcastanedac@unal.edu.co

In this paper, we investigate the effects of helical primordial magnetic fields (PMFs) on the cosmic microwave background (CMB) reduced bispectrum. We derive the full three-point statistics of helical magnetic fields and numerically calculate the even contribution in the collinear configuration. We then numerically compute the CMB reduced bispectrum induced by passive and compensated PMF modes on large angular scales. There is a negative signal on the bispectrum due to the helical terms of the fields and we also observe that the biggest contribution to the bispectrum comes from the non-zero IR cut-off for causal fields, unlike the two-point correlationmore » case. For negative spectral indices, the reduced bispectrum is enhanced by the passive modes. This gives a lower value of the upper limit for the mean amplitude of the magnetic field on a given characteristic scale. However, high values of IR cut-off in the bispectrum, and the helical terms of the magnetic field relaxes this bound. This demonstrates the importance of the IR cut-off and helicity in the study of the nature of PMFs from CMB observations.« less

Structure-activity relationship study of Aib-containing amphipathic helical peptide-cyclic RGD conjugates as carriers for siRNA delivery.

PubMed

Wada, Shun-Ichi; Takesada, Anna; Nagamura, Yurie; Sogabe, Eri; Ohki, Rieko; Hayashi, Junsuke; Urata, Hidehito

2017-12-15

The conjugation of Aib-containing amphipathic helical peptide with cyclo(-Arg-Gly-Asp-d-Phe-Cys-) (cRGDfC) at the C-terminus of the helix peptide (PI) has been reported to be useful for constructing a carrier for targeted siRNA delivery into cells. In order to explore structure-activity relationships for the development of potential carriers for siRNA delivery, we synthesized conjugates of Aib-containing amphipathic helical peptide with cRGDfC at the N-terminus (PII) and both the N- and C-termini (PIII) of the helical peptide. Furthermore, to examine the influence of PI helical chain length on siRNA delivery, truncated peptides containing 16 (PIV), 12 (PV), and 8 (PVI) amino acid residues at the N-terminus of the helical chain were synthesized. PII and PIII, as well as PI, could deliver anti-luciferase siRNA into cells to induce the knockdown of luciferase stably expressed in cells. In contrast, all of the truncated peptides were unlikely to transport siRNA into cells. Copyright © 2017 Elsevier Ltd. All rights reserved.

Iron(II) supramolecular helicates condense plasmid DNA and inhibit vital DNA-related enzymatic activities.

PubMed

Malina, Jaroslav; Hannon, Michael J; Brabec, Viktor

2015-07-27

The dinuclear iron(II) supramolecular helicates [Fe2 L3 ]Cl4 (L=C25 H20 N4 ) bind to DNA through noncovalent (i.e., hydrogen-bonding, electrostatic) interactions and exhibit antimicrobial and anticancer effects. In this study, we show that the helicates condense plasmid DNA with a much higher potency than conventional DNA-condensing agents. Notably, molecules of DNA in the presence of the M enantiomer of [Fe2 L3 ]Cl4 do not form intermolecular aggregates typically formed by other condensing agents, such as spermidine or spermine. The helicates inhibit the activity of several DNA-processing enzymes, such as RNA polymerase, DNA topoisomerase I, deoxyribonuclease I, and site-specific restriction endonucleases. However, the results also indicate that the DNA condensation induced by the helicates does not play a crucial role in these inhibition reactions. The mechanisms for the inhibitory effects of [Fe2 L3 ]Cl4 helicates on DNA-related enzymatic activities have been proposed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Expanding Non-solenoidal Startup with Local Helicity Injection to Increased Toroidal Field and Helicity Injection Rate

NASA Astrophysics Data System (ADS)

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

2015-11-01

Local helicity injection (LHI) is a non-solenoidal startup technique under development on the Pegasus ST. Plasma currents up to 0.18 MA have been initiated by LHI in conjunction with poloidal field induction. A 0-D power balance model has been developed to predict plasma current evolution by balancing helicity input against resistive dissipation. The model is being validated against a set of experimental measurements and magnetic reconstructions with radically varied plasma geometric evolutions. Outstanding physics issues with LHI startup are the scalings of confinement and MHD activity with helicity injection rate and toroidal field strength, as well as injector behavior at high field. Preliminary results from the newly-installed Thomson scattering system suggest core temperatures of a few hundred eV during LHI startup. Measurements are being expanded to multiple spatial points for ongoing confinement studies. A set of larger-area injectors is being installed in the lower divertor region, where increased toroidal field will provide a helicity injection rate over 3 times that of outboard injectors. In this regime helicity injection will be the dominant current drive. Experiments with divertor injectors will permit experimental differentiation of several possible confinement models, and demonstrate the feasibility of LHI startup at high field. Work supported by US DOE grant DE-FG02-96ER54375.

Public Data Set: Radially Scanning Magnetic Probes to Study Local Helicity Injection Dynamics

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

Richner, Nathan J; Bongard, Michael W; Fonck, Raymond J

This data set contains openly-documented, machine readable digital research data corresponding to figures published in N.J. Richner et al., 'Radially Scanning Magnetic Probes to Study Local Helicity Injection Dynamics,' accepted for publication in Rev. Sci. Instrum (2018).

Non-solenoidal startup and low-β operations in Pegasus

NASA Astrophysics Data System (ADS)

Schlossberg, D. J.; Battaglia, D. J.; Bongard, M. W.; Fonck, R. J.; Redd, A. J.

2009-11-01

Non-solenoidal startup using point-source DC helicity injectors (plasma guns) has been achieved in the Pegasus Toroidal Experiment for plasmas with Ip in excess of 100 kA using Iinj<4,A. The maximum achieved Ip tentatively scales as √ITFIinj/w, where w is the radial thickness of the gun-driven edge. The Ip limits appear to conform to a simple stationary model involving helicity conservation and Taylor relaxation. However, observed MHD activity reveals the additional dynamics of the relaxation process, evidenced by intermittent bursts of n=1 activity correlated with rapid redistribution of the current channel. Recent upgrades to the gun system provide higher helicity injection rates, smaller w, a more constrained gun current path, and more precise diagnostics. Experimental goals include extending parametric scaling studies, determining the conditions where parallel conduction losses dominate the helicity dissipation, and building the physics understanding of helicity injection to confidently design gun systems for larger, future tokamaks.

Macroscopic ordering of helical pores for arraying guest molecules noncentrosymmetrically

PubMed Central

Li, Chunji; Cho, Joonil; Yamada, Kuniyo; Hashizume, Daisuke; Araoka, Fumito; Takezoe, Hideo; Aida, Takuzo; Ishida, Yasuhiro

2015-01-01

Helical nanostructures have attracted continuous attention, not only as media for chiral recognition and synthesis, but also as motifs for studying intriguing physical phenomena that never occur in centrosymmetric systems. To improve the quality of signals from these phenomena, which is a key issue for their further exploration, the most straightforward is the macroscopic orientation of helices. Here as a versatile scaffold to rationally construct this hardly accessible structure, we report a polymer framework with helical pores that unidirectionally orient over a large area (∼10 cm2). The framework, prepared by crosslinking a supramolecular liquid crystal preorganized in a magnetic field, is chemically robust, functionalized with carboxyl groups and capable of incorporating various basic or cationic guest molecules. When a nonlinear optical chromophore is incorporated in the framework, the resultant complex displays a markedly efficient nonlinear optical output, owing to the coherence of signals ensured by the macroscopically oriented helical structure. PMID:26416086

Water-Solubilized, Cap-Stabilized, Helical Polyalanines: Calibration Standards for NMR and CD Analyses

PubMed Central

Heitmann, Björn; Job, Gabriel E.; Kennedy, Robert J.; Walker, Sharon M.; Kemp, Daniel S.

2006-01-01

NMR and CD studies are reported for two length series of solubilized, spaced, highly helical polyalanines that are N-capped by the optimal helix stabilizer βAsp-Hel and C-capped by β-aminoalanine beta and that are studied in water at 2 °C, pH 1–8. NMR analysis yields a structural characterization of the peptide AcβAspHelAla8betaNH2 and selected members of one βAspHelAlanbeta series. At pH > 4.5 the βAspHel cap provides a preorganized triad of carboxylate anion and two amide residues that is complementary to the helical polyalanine N-terminus. The C-terminal β-aminoalanine assumes a helix-stabilizing conformation consistent with literature precedents. H(N)CO NMR experiments applied to capped, uniformly 13C- and 15N-labeled Ala8 and Ala12 peptides define Alan hydrogen bonding signatures as α-helical without detectable 310 character. Relative NH→ND exchange rates yield site protection factors PFi that define uniquely high fractional helicities FH for the peptide Alan regions. These Alan calibration series, studied in water and lacking helix-stabilizing tertiary structure, yield the first 13C NMR chemical shifts, 3JHNHα coupling constants, and CD ellipticities [θMolar]λ,n characteristic of a fully helical alanine within an Alan context. CD data are used to assign parameters X and [θ]λ,∞, required for rigorous calculation of FH values from CD ellipticities. PMID:15701003

Reverse total shoulder arthroplasty using helical blade to optimize glenoid fixation and bone preservation: preliminary results in thirty five patients with minimum two year follow-up.

PubMed

Zilber, Sebastien; Camana, Eleonora; Lapner, Peter; Haritinian, Emil; Nove Josserand, Laurent

2018-03-26

Glenoid loosening is a common cause of reverse total shoulder arthroplasty (RTSA) failure, and grafting of the glenoid is often required for revision due to bone loss due to the central peg in most glenoid baseplates. Helical blades have been used in the hip to optimize bone fixation in proximal femoral fracture. This study presents the initial results of specifically designed helical blade in the shoulder to optimize glenoid bone fixation and preservation as part of RTSA. Thirty-five patients underwent RTSA with glenoid helical blade fixation. An uncemented glenoid baseplate was used with a central helical blade partially coated with hydroxyapatite and two or three screws. Outcome analysis was performed pre-operatively and at two years. All patients were satisfied with the results and significant improvement was observed in functional outcome scores between baseline and final follow-up. There was a single intra-operative undisplaced glenoid fracture which did not compromise the baseplate fixation. There was no radiographic evidence of loosening or radiolucencies around the helical blade. The helical blade provides a satisfactory primary fixation. Because of its length (21 mm), care should be taken in cases of pre-existing bone loss or sclerotic bone to avoid glenoid fracture or anterior cortical perforation. Helical blade has the potential to facilitate glenoid implant revision by preserving the glenoid bone stock.

Impact of helical boundary conditions in MHD modeling of RFP and tokamak plasmas

NASA Astrophysics Data System (ADS)

Bonfiglio, D.; Cappello, S.; Escande, D. F.; Piovesan, P.; Veranda, M.; Chacón, L.

2012-10-01

Helical boundary conditions imposed by the active control system of the RFX-mod device provide a handle to govern the plasma dynamics in both RFP and Ohmic tokamak discharges [1]. By applying an edge radial magnetic field with proper helicity, it is possible to increase the persistence of the spontaneous helical RFP states at high current,and to stimulate them also at low current or high density. Helical BCs even allow to access helical states with different helicity than the spontaneous one [2]. In Ohmic tokamak operation at q(a)<2, the presence of the 2/1 RWM reduces the sawtoothing activity of the 1/1 internal kink, which takes a stationary snake-like character instead. Many of these features are qualitatively reproduced in 3D nonlinear MHD modeling. We study the impact of helical BCs on the MHD dynamics in both RFP and tokamak with two successfully benchmarked numerical tools, SpeCyl and PIXIE3D [3]. We recover the bifurcation from a sawtooth to a snake solution when imposing a 2/1 BC in the tokamak case and we interpret this as a toroidal/nonlinear coupling effect. We show that the bifurcation is more easily stimulated with a 1/1 BC.[4pt] [1] P. Piovesan, invited talk this meeting[0pt] [2] M. Veranda et al EPS-ICPP Conference (2012) P4.004[0pt] [3] D. Bonfiglio et al Phys. Plasmas (2010)

Implant breast reconstruction followed by radiotherapy: Can helical tomotherapy become a standard irradiation treatment?

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

Massabeau, Carole, E-mail: cmassabeau@hotmail.com; Fournier-Bidoz, Nathalie; Wakil, Georges

2012-01-01

To evaluate the benefits and limitations of helical tomotherapy (HT) for loco-regional irradiation of patients after a mastectomy and immediate implant-based reconstruction. Ten breast cancer patients with retropectoral implants were randomly selected for this comparative study. Planning target volumes (PTVs) 1 (the volume between the skin and the implant, plus margin) and 2 (supraclavicular, infraclavicular, and internal mammary nodes, plus margin) were 50 Gy in 25 fractions using a standard technique and HT. The extracted dosimetric data were compared using a 2-tailed Wilcoxon matched-pair signed-rank test. Doses for PTV1 and PTV2 were significantly higher with HT (V95 of 98.91 andmore » 97.91%, respectively) compared with the standard technique (77.46 and 72.91%, respectively). Similarly, the indexes of homogeneity were significantly greater with HT (p = 0.002). HT reduced ipsilateral lung volume that received {>=}20 Gy (16.7 vs. 35%), and bilateral lungs (p = 0.01) and neighboring organs received doses that remained well below tolerance levels. The heart volume, which received 25 Gy, was negligible with both techniques. HT can achieve full target coverage while decreasing high doses to the heart and ipsilateral lung. However, the low doses to normal tissue volumes need to be reduced in future studies.« less

Scale Dependence of Magnetic Helicity in the Solar Wind

NASA Technical Reports Server (NTRS)

Brandenburg, Axel; Subramanian, Kandaswamy; Balogh, Andre; Goldstein, Melvyn L.

2011-01-01

We determine the magnetic helicity, along with the magnetic energy, at high latitudes using data from the Ulysses mission. The data set spans the time period from 1993 to 1996. The basic assumption of the analysis is that the solar wind is homogeneous. Because the solar wind speed is high, we follow the approach first pioneered by Matthaeus et al. by which, under the assumption of spatial homogeneity, one can use Fourier transforms of the magnetic field time series to construct one-dimensional spectra of the magnetic energy and magnetic helicity under the assumption that the Taylor frozen-in-flow hypothesis is valid. That is a well-satisfied assumption for the data used in this study. The magnetic helicity derives from the skew-symmetric terms of the three-dimensional magnetic correlation tensor, while the symmetric terms of the tensor are used to determine the magnetic energy spectrum. Our results show a sign change of magnetic helicity at wavenumber k approximately equal to 2AU(sup -1) (or frequency nu approximately equal to 2 microHz) at distances below 2.8AU and at k approximately equal to 30AU(sup -1) (or nu approximately equal to 25 microHz) at larger distances. At small scales the magnetic helicity is positive at northern heliographic latitudes and negative at southern latitudes. The positive magnetic helicity at small scales is argued to be the result of turbulent diffusion reversing the sign relative to what is seen at small scales at the solar surface. Furthermore, the magnetic helicity declines toward solar minimum in 1996. The magnetic helicity flux integrated separately over one hemisphere amounts to about 10(sup 45) Mx(sup 2) cycle(sup -1) at large scales and to a three times lower value at smaller scales.

Self-assembly of a double-helical complex of sodium.

PubMed

Bell, T W; Jousselin, H

1994-02-03

Spontaneous self-organization of helical and multiple-helical molecular structures occurs on several levels in living organisms. Key examples are alpha-helical polypeptides, double-helical nucleic acids and helical protein structures, including F-actin, microtubules and the protein sheath of the tobacco mosaic virus. Although the self-assembly of double-helical transition-metal complexes bears some resemblance to the molecular organization of double-stranded DNA, selection between monohelical, double-helical and triple-helical structures is determined largely by the size and geometrical preference of the tightly bound metal. Here we present an example of double-helical assembly induced by the weaker and non-directional interactions of an alkali-metal ion with an organic ligand that is pre-organized into a coil. We have characterized the resulting complex by two-dimensional NMR and fast-atom-bombardment mass spectrometry. These results provide a step toward the creation of molecular tubes or ion channels consisting of intertwined coils.

Anti-infective activity of apolipoprotein domain derived peptides in vitro: identification of novel antimicrobial peptides related to apolipoprotein B with anti-HIV activity

PubMed Central

2010-01-01

Background Previous reports have shown that peptides derived from the apolipoprotein E receptor binding region and the amphipathic α-helical domains of apolipoprotein AI have broad anti-infective activity and antiviral activity respectively. Lipoproteins and viruses share a similar cell biological niche, being of overlapping size and displaying similar interactions with mammalian cells and receptors, which may have led to other antiviral sequences arising within apolipoproteins, in addition to those previously reported. We therefore designed a series of peptides based around either apolipoprotein receptor binding regions, or amphipathic α-helical domains, and tested these for antiviral and antibacterial activity. Results Of the nineteen new peptides tested, seven showed some anti-infective activity, with two of these being derived from two apolipoproteins not previously used to derive anti-infective sequences. Apolipoprotein J (151-170) - based on a predicted amphipathic alpha-helical domain from apolipoprotein J - had measurable anti-HSV1 activity, as did apolipoprotein B (3359-3367) dp (apoBdp), the latter being derived from the LDL receptor binding domain B of apolipoprotein B. The more active peptide - apoBdp - showed similarity to the previously reported apoE derived anti-infective peptide, and further modification of the apoBdp sequence to align the charge distribution more closely to that of apoEdp or to introduce aromatic residues resulted in increased breadth and potency of activity. The most active peptide of this type showed similar potent anti-HIV activity, comparable to that we previously reported for the apoE derived peptide apoEdpL-W. Conclusions These data suggest that further antimicrobial peptides may be obtained using human apolipoprotein sequences, selecting regions with either amphipathic α-helical structure, or those linked to receptor-binding regions. The finding that an amphipathic α-helical region of apolipoprotein J has antiviral activity comparable with that for the previously reported apolipoprotein AI derived peptide 18A, suggests that full-length apolipoprotein J may also have such activity, as has been reported for full-length apolipoprotein AI. Although the strength of the anti-infective activity of the sequences identified was limited, this could be increased substantially by developing related mutant peptides. Indeed the apolipoprotein B-derived peptide mutants uncovered by the present study may have utility as HIV therapeutics or microbicides. PMID:20298574

Helical 4D CT and Comparison with Cine 4D CT

NASA Astrophysics Data System (ADS)

Pan, Tinsu

4D CT was one of the most important developments in radiation oncology in the last decade. Its early development in single slice CT and commercialization in multi-slice CT has radically changed our practice in radiation treatment of lung cancer, and has enabled the stereotactic radiosurgery of early stage lung cancer. In this chapter, we will document the history of 4D CT development, detail the data sufficiency condition governing the 4D CT data collection; present the design of the commercial helical 4D CTs from Philips and Siemens; compare the differences between the helical 4D CT and the GE cine 4D CT in data acquisition, slice thickness, acquisition time and work flow; review the respiratory monitoring devices; and understand the causes of image artifacts in 4D CT.

Successive Homologous Coronal Mass Ejections Driven by Shearing and Converging Motions in Solar Active Region NOAA 12371

NASA Astrophysics Data System (ADS)

Vemareddy, P.

2017-08-01

We study the magnetic field evolution in AR 12371, related to its successive eruptive nature. During the disk transit of seven days, the active region (AR) launched four sequential fast coronal mass ejections (CMEs), which are associated with long duration M-class flares. Morphological study delineates a pre-eruptive coronal sigmoid structure above the polarity inversion line (PIL) similar to Moore et al.’s study. The velocity field derived from tracked magnetograms indicates persistent shear and converging motions of polarity regions about the PIL. While these shear motions continue, the crossed arms of two sigmoid elbows are being brought to interaction by converging motions at the middle of the PIL, initiating the tether-cutting reconnection of field lines and the onset of the CME explosion. The successive CMEs are explained by a cyclic process of magnetic energy storage and release referred to as “sigmoid-to-arcade-to-sigmoid” transformation driven by photospheric flux motions. Furthermore, the continued shear motions inject helicity flux with a dominant negative sign, which contributes to core field twist and its energy by building a twisted flux rope (FR). After a limiting value, the excess coronal helicity is expelled by bodily ejection of the FR, which is initiated by some instability as realized by intermittent CMEs. This AR is in contrast with the confined AR 12192 with a predominant negative sign and larger helicity flux, but much weaker (-0.02 turns) normalized coronal helicity content. While predominant signed helicity flux is a requirement for CME eruption, our study suggests that the magnetic flux normalized helicity flux is a necessary condition accommodating the role of background flux and appeals to a further study of a large sample of ARs.

Successive Homologous Coronal Mass Ejections Driven by Shearing and Converging Motions in Solar Active Region NOAA 12371

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

Vemareddy, P., E-mail: vemareddy@iiap.res.in

We study the magnetic field evolution in AR 12371, related to its successive eruptive nature. During the disk transit of seven days, the active region (AR) launched four sequential fast coronal mass ejections (CMEs), which are associated with long duration M-class flares. Morphological study delineates a pre-eruptive coronal sigmoid structure above the polarity inversion line (PIL) similar to Moore et al.’s study. The velocity field derived from tracked magnetograms indicates persistent shear and converging motions of polarity regions about the PIL. While these shear motions continue, the crossed arms of two sigmoid elbows are being brought to interaction by convergingmore » motions at the middle of the PIL, initiating the tether-cutting reconnection of field lines and the onset of the CME explosion. The successive CMEs are explained by a cyclic process of magnetic energy storage and release referred to as “sigmoid-to-arcade-to-sigmoid” transformation driven by photospheric flux motions. Furthermore, the continued shear motions inject helicity flux with a dominant negative sign, which contributes to core field twist and its energy by building a twisted flux rope (FR). After a limiting value, the excess coronal helicity is expelled by bodily ejection of the FR, which is initiated by some instability as realized by intermittent CMEs. This AR is in contrast with the confined AR 12192 with a predominant negative sign and larger helicity flux, but much weaker (−0.02 turns) normalized coronal helicity content. While predominant signed helicity flux is a requirement for CME eruption, our study suggests that the magnetic flux normalized helicity flux is a necessary condition accommodating the role of background flux and appeals to a further study of a large sample of ARs.« less

The role of proline residues in the dynamics of transmembrane helices: the case of bacteriorhodopsin.

PubMed

Perálvarez-Marín, Alex; Bourdelande, José-Luis; Querol, Enric; Padrós, Esteve

2006-01-01

Proline residues in transmembrane helices have been found to have important roles in the functioning of membrane proteins. Moreover, Pro residues occur with high frequency in transmembrane alpha-helices, as compared to alpha-helices for soluble proteins. Here, we report several properties of the bacteriorhodopsin mutants P50A (helix B), P91A (helix C) and P186A (helix F). Compared to wild type, strongly perturbed behaviour has been found for these mutants. In the resting state, increased hydroxylamine accessibility and altered Asp-85 pKa and light-dark adaptation were observed. On light activation, hydroxylamine accessibility was increased and proton transport activity, M formation kinetics and FTIR difference spectra of M and N intermediates showed clear distortions. On the basis of these alterations and the near identity of the crystalline structures of mutants with that of wild type, we conclude that the transmembrane proline residues of bacteriorhodopsin fulfil a dynamic role in both the resting and the light-activated states. Our results are consistent with the notion that mutation of Pro to Ala allows the helix to increase its flexibility towards the direction originally hindered by the steric clash between the ring Cgamma and the carbonyl O of the i-4 residue, at the same time decreasing the mobility towards the opposite direction. Due to their properties, transmembrane Pro residues may serve as transmission elements of conformational changes during the transport process. We propose that these concepts can be extended to other transmembrane proteins.

Some consequences of shear on galactic dynamos with helicity fluxes

NASA Astrophysics Data System (ADS)

Zhou, Hongzhe; Blackman, Eric G.

2017-08-01

Galactic dynamo models sustained by supernova (SN) driven turbulence and differential rotation have revealed that the sustenance of large-scale fields requires a flux of small-scale magnetic helicity to be viable. Here we generalize a minimalist analytic version of such galactic dynamos to explore some heretofore unincluded contributions from shear on the total turbulent energy and turbulent correlation time, with the helicity fluxes maintained by either winds, diffusion or magnetic buoyancy. We construct an analytic framework for modelling the turbulent energy and correlation time as a function of SN rate and shear. We compare our prescription with previous approaches that include only rotation. The solutions depend separately on the rotation period and the eddy turnover time and not just on their ratio (the Rossby number). We consider models in which these two time-scales are allowed to be independent and also a case in which they are mutually dependent on radius when a radial-dependent SN rate model is invoked. For the case of a fixed rotation period (or a fixed radius), we show that the influence of shear is dramatic for low Rossby numbers, reducing the correlation time of the turbulence, which, in turn, strongly reduces the saturation value of the dynamo compared to the case when the shear is ignored. We also show that even in the absence of winds or diffusive fluxes, magnetic buoyancy may be able to sustain sufficient helicity fluxes to avoid quenching.

Helical localized wave solutions of the scalar wave equation.

PubMed

Overfelt, P L

2001-08-01

A right-handed helical nonorthogonal coordinate system is used to determine helical localized wave solutions of the homogeneous scalar wave equation. Introducing the characteristic variables in the helical system, i.e., u = zeta - ct and v = zeta + ct, where zeta is the coordinate along the helical axis, we can use the bidirectional traveling plane wave representation and obtain sets of elementary bidirectional helical solutions to the wave equation. Not only are these sets bidirectional, i.e., based on a product of plane waves, but they may also be broken up into right-handed and left-handed solutions. The elementary helical solutions may in turn be used to create general superpositions, both Fourier and bidirectional, from which new solutions to the wave equation may be synthesized. These new solutions, based on the helical bidirectional superposition, are members of the class of localized waves. Examples of these new solutions are a helical fundamental Gaussian focus wave mode, a helical Bessel-Gauss pulse, and a helical acoustic directed energy pulse train. Some of these solutions have the interesting feature that their shape and localization properties depend not only on the wave number governing propagation along the longitudinal axis but also on the normalized helical pitch.

Helical prospective ECG-gating in cardiac computed tomography: radiation dose and image quality.

PubMed

DeFrance, Tony; Dubois, Eric; Gebow, Dan; Ramirez, Alex; Wolf, Florian; Feuchtner, Gudrun M

2010-01-01

Helical prospective ECG-gating (pECG) may reduce radiation dose while maintaining the advantages of helical image acquisition for coronary computed tomography angiography (CCTA). Aim of this study was to evaluate helical pECG-gating in CCTA in regards to radiation dose and image quality. 86 patients undergoing 64-multislice CCTA were enrolled. pECG-gating was performed in patients with regular heart rates (HR) < 65 bpm; with the gating window set at 70-85% of the cardiac cycle. All patients received oral and some received additional IV beta-blockers to achieve HR < 65 bpm. In patients with higher or irregular HR, or for functional evaluation, retrospective ECG-gating (rECG) was performed. The average X-ray dose was estimated from the dose length product. Each arterial segment (modified AHA/ACC 17-segment-model) was evaluated on a 4-point image quality scale (4 = excellent; 3 = good, mild artefact; 2 = acceptable, some artefact, 1 = uninterpretable). pECG-gating was applied in 57 patients, rECG-gating in 29 patients. There was no difference in age, gender, body mass index, scan length or tube output settings between both groups. HR in the pECG-group was 54.7 bpm (range, 43-64). The effective radiation dose was significantly lower for patients scanned with pECG-gating with mean 6.9 mSv +/- 1.9 (range, 2.9-10.7) compared to rECG with 16.9 mSv +/- 4.1 (P < 0.001), resulting in a mean dose reduction of 59.2%. For pECG-gating, out of 969 coronary segments, 99.3% were interpretable. Image quality was excellent in 90.2%, good in 7.8%, acceptable in 1.3% and non-interpretable in 0.7% (n = 7 segments). For patients with steady heart rates <65 bpm, helical prospective ECG-gating can significantly lower the radiation dose while maintaining high image quality.

Secondary Structures of Ubiquitin Ions Soft-Landed onto Self-Assembled Monolayer Surfaces

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

Hu, Qichi; Laskin, Julia

2016-06-09

The secondary structures of multiply charged ubiquitin ions soft-landed onto self-assembled monolayer (SAM) surfaces were studied using in situ infrared reflection-absorption spectroscopy (IRRAS). Two charge states of ubiquitin, 5+ and 13+, were mass selected separately from a mixture of different charge states produced by electrospray ionization (ESI). The low 5+ charge state represents a native-like folded state of ubiquitin, while the high 13+ charge state assumes an extended, almost linear conformation. Each of the two charge states was soft-landed onto a CH 3- and COOH-terminated SAM of alkylthiols on gold (HSAM and COOH-SAM). HSAM is a hydrophobic surface known tomore » stabilize helical conformations of soft-landed protonated peptides, whereas COOH-SAM is a hydrophilic surface that preferentially stabilizes β-sheet conformations. IRRAS spectra of the soft-landed ubiquitin ions were acquired as a function of time during and after ion soft-landing. Similar to smaller peptide ions, helical conformations of ubiquitin are found to be more abundant on HSAM, while the relative abundance of β-sheet conformations increases on COOH-SAM. The initial charge state of ubiquitin also has a pronounced effect on its conformation on the surface. Specifically, on both surfaces, a higher relative abundance of helical conformations and lower relative abundance of β-sheet conformations is observed for the 13+ charge state compared to the 5+ charge state. Time-resolved experiments indicate that the α-helical band in the spectrum of the 13+ charge state slowly increases with time on the HSAM surface and decreases in the spectrum of the 13+ charge state on COOH-SAM. These results further support the preference of the hydrophobic HSAM surface toward helical conformations and demonstrate that soft-landed protein ions may undergo slow conformational changes during and after deposition.« less

The Contribution of Interchain Salt Bridges to Triple-Helical Stability in Collagen

PubMed Central

Gurry, Thomas; Nerenberg, Paul S.; Stultz, Collin M.

2010-01-01

Abstract Studies on collagen and collagen-like peptides suggest that triple-helical stability can vary along the amino acid chain. In this regard, it has been shown that lysine residues in the Y position and acidic residues in the X′ position of (GPO)3GXYGX′Y′(GPO)3 peptides lead to triple-helical structures with melting temperatures similar to (GPO)8 (where O is hydroxyproline), which is generally regarded as the most stable collagen-like sequence of this length. This enhanced stability has been attributed to the formation of salt bridges between adjacent collagen chains. In this study, we explore the relationship between interchain salt bridge formation and triple-helical stability using detailed molecular simulations. Although our results confirm that salt bridges promote triple-helical stability, we find that not all salt bridges are created equal. In particular, lysine-glutamate salt bridges are most stabilizing when formed between residues in the middle strand (B) and the trailing strand (C), whereas lysine-aspartate salt bridges are most stabilizing when formed between residues in the leading (A) and middle (B) strand—the latter observation being consistent with recent NMR data on a heterotrimeric model peptide. Overall, we believe these data clarify the role of salt bridges in modulating triple-helical stability and can be used to guide the design of collagen-like peptides that have specific interchain interactions. PMID:20513408

Usefulness of axial planes of helical computed tomography for diagnosis of pancreaticobiliary maljunction in early infants with negative findings on magnetic resonance cholangiopancreatography.

PubMed

Okada, Tadao; Sasaki, Fumiaki; Honda, Shouhei; Naitou, Satsuki; Onodera, Yuya; Todo, Satoru

2008-03-01

Magnetic resonance cholangiopancreatography (MRCP) is not sufficient to detect pancreaticobiliary maljunction (PBM) in young infants because the main pancreatic duct is not visualized and respiratory artifacts occur. To our knowledge, there are no reports highlighting the diagnostic accuracy of evaluation using the axial planes of helical computed tomographic (CT) scanning with contrast medium instead of 3-dimensional (3D) reconstruction. The aim of this study was to describe our experience and the characteristics of 3 children with PBM diagnosed using the axial planes of helical CT with contrast medium, although they showed negative findings of PBM by MRCP, instead of 3D reconstruction. Three patients aged from 1 month to 3 years were diagnosed with PBM using the axial planes of helical CT with contrast medium though MRCP could not show the common channel and/or the entrance of the common channel into the duodenum. In all 3 patients, PBM of the common channel was not revealed by MRCP. On the other hand, axial planes of contrast-enhanced helical CT scans showed PBM clearly. Our experience suggests that axial planes of the contrast-enhanced helical CT scan comprise an accurate tool for the diagnosis of fusiform-type PBM and could replace MRCP in younger children. Further studies are necessary for better assessment of the potential advantages and pitfalls of this modality.

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.

Magnetic helicity conservation and inverse energy cascade in electron magnetohydrodynamic wave packets.

PubMed

Cho, Jungyeon

2011-05-13

Electron magnetohydrodynamics (EMHD) provides a fluidlike description of small-scale magnetized plasmas. An EMHD wave propagates along magnetic field lines. The direction of propagation can be either parallel or antiparallel to the magnetic field lines. We numerically study propagation of three-dimensional (3D) EMHD wave packets moving in one direction. We obtain two major results. (1) Unlike its magnetohydrodynamic (MHD) counterpart, an EMHD wave packet is dispersive. Because of this, EMHD wave packets traveling in one direction create opposite-traveling wave packets via self-interaction and cascade energy to smaller scales. (2) EMHD wave packets traveling in one direction clearly exhibit inverse energy cascade. We find that the latter is due to conservation of magnetic helicity. We compare inverse energy cascade in 3D EMHD turbulence and two-dimensional (2D) hydrodynamic turbulence.

Probing the Role of Nascent Helicity in p27 Function as a Cell Cycle Regulator

PubMed Central

Otieno, Steve; Kriwacki, Richard

2012-01-01

p27 regulates the activity of Cdk complexes which are the principal governors of phase transitions during cell division. Members of the p27 family of proteins, which also includes p21 and p57, are called the Cip/Kip cyclin-dependent kinase regulators (CKRs). Interestingly, the Cip/Kip CKRs play critical roles in cell cycle regulation by being intrinsically unstructured, a characteristic contrary to the classical structure-function paradigm. They exhibit nascent helicity which has been localized to a segment referred to as sub-domain LH. The nascent helicity of this sub-domain is conserved and we hypothesize that it is an important determinant of their functional properties. To test this hypothesis, we successfully designed and prepared p27 variants in which domain LH was either more or less helical with respect to the wild-type protein. Thermal denaturation experiments showed that the ternary complexes of the p27 variants bound to Cdk2/Cyclin A were less stable compared to the wild-type complex. Isothermal titration calorimetry experiments showed a decrease in the enthalpy of binding for all the mutants with respect to p27. The free energies of binding varied within a much narrower range. In vitro Cdk2 inhibition assays showed that the p27 variants exhibited disparate inhibitory potencies. Furthermore, when over-expressed in NIH 3T3 mouse fibroblast cells, the less helical p27 variants were less effective in causing cell cycle arrest relative to the wild-type p27. Our results indicate that the nascent helicity of sub-domain LH plays a key role mediating the biological function of p27. PMID:23071750

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

PubMed

Leader, David P; Milner-White, E James

2011-03-01

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

Tomographic reconstruction of heat release rate perturbations induced by helical modes in turbulent swirl flames

NASA Astrophysics Data System (ADS)

Moeck, Jonas P.; Bourgouin, Jean-François; Durox, Daniel; Schuller, Thierry; Candel, Sébastien

2013-04-01

Swirl flows with vortex breakdown are widely used in industrial combustion systems for flame stabilization. This type of flow is known to sustain a hydrodynamic instability with a rotating helical structure, one common manifestation of it being the precessing vortex core. The role of this unsteady flow mode in combustion is not well understood, and its interaction with combustion instabilities and flame stabilization remains unclear. It is therefore important to assess the structure of the perturbation in the flame that is induced by this helical mode. Based on principles of tomographic reconstruction, a method is presented to determine the 3-D distribution of the heat release rate perturbation associated with the helical mode. Since this flow instability is rotating, a phase-resolved sequence of projection images of light emitted from the flame is identical to the Radon transform of the light intensity distribution in the combustor volume and thus can be used for tomographic reconstruction. This is achieved with one stationary camera only, a vast reduction in experimental and hardware requirements compared to a multi-camera setup or camera repositioning, which is typically required for tomographic reconstruction. Different approaches to extract the coherent part of the oscillation from the images are discussed. Two novel tomographic reconstruction algorithms specifically tailored to the structure of the heat release rate perturbations related to the helical mode are derived. The reconstruction techniques are first applied to an artificial field to illustrate the accuracy. High-speed imaging data acquired in a turbulent swirl-stabilized combustor setup with strong helical mode oscillations are then used to reconstruct the 3-D structure of the associated perturbation in the flame.

Design of an α-helical antimicrobial peptide with improved cell-selective and potent anti-biofilm activity

PubMed Central

Zhang, Shi-Kun; Song, Jin-wen; Gong, Feng; Li, Su-Bo; Chang, Hong-Yu; Xie, Hui-Min; Gao, Hong-Wei; Tan, Ying-Xia; Ji, Shou-Ping

2016-01-01

AR-23 is a melittin-related peptide with 23 residues. Like melittin, its high α-helical amphipathic structure results in strong bactericidal activity and cytotoxicity. In this study, a series of AR-23 analogues with low amphipathicity were designed by substitution of Ala1, Ala8 and Ile17 with positively charged residues (Arg or Lys) to study the effect of positively charged residue distribution on the biological viability of the antimicrobial peptide. Substitution of Ile17 on the nonpolar face with positively charged Lys dramatically altered the hydrophobicity, amphipathicity, helicity and the membrane-penetrating activity against human cells as well as the haemolytic activity of the peptide. However, substitution on the polar face only slightly affected the peptide biophysical properties and biological activity. The results indicate that the position rather than the number of positively charged residue affects the biophysical properties and selectivity of the peptide. Of all the analogues, A(A1R, A8R, I17K), a peptide with Ala1-Arg, Ala8-Arg and Ile17-Lys substitutions, exhibited similar bactericidal activity and anti-biofilm activity to AR-23 but had much lower haemolytic activity and cytotoxicity against mammalian cells compared with AR-23. Therefore, the findings reported here provide a rationalization for peptide design and optimization, which will be useful for the future development of antimicrobial agents. PMID:27271216

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

Heat transfer and pressure drop studies of TiO2/DI water nanofluids in helically corrugated tubes using spiraled rod inserts

NASA Astrophysics Data System (ADS)

Anbu, S.; Venkatachalapathy, S.; Suresh, S.

2018-05-01

An experimental study on the convective heat transfer and friction factor characteristics of TiO2/DI water nanofluids in uniformly heated plain and helically corrugated tubes (HCT) with and without spiraled rod inserts (SRI) under laminar flow regime is presented in this paper. TiO2 nanoparticles with an average size of 32 nm are dispersed in deionized (DI) water to form stable suspensions containing 0.1, 0.15, 0.2, and 0.25% volume concentrations of nanoparticles. It is found that the inclusion of nanoparticles to DI water ameliorated Nusselt number which increased with nanoparticles concentration upto 0.2%. Two spiraled rod inserts made of copper with different pitches (pi = 50 mm and 30 mm) are inserted in both plain and corrugated tubes and it is found that the addition of these inserts increased the Nusselt number substantially. For Helically corrugated tube with lower pitch and maximum height of corrugation (pc = 8 mm, hc = 1 mm) with 0.2% volume concentration of nanoparticles, a maximum enhancement of 15% in Nusselt number is found without insert and with insert having lower pitch (pi = 30 mm) the enhancement is 34% when compared to DI water in plain tube. The results on friction factor show a maximum penalty of about 53.56% for the above HCT.

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

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.

Hemispheric Patterns in Electric Current Helicity of Solar Magnetic Fields During Solar Cycle 24: Results from SOLIS, SDO and Hinode

NASA Astrophysics Data System (ADS)

Gusain, S.

2017-12-01

We study the hemispheric patterns in electric current helicity distribution on the Sun. Magnetic field vector in the photosphere is now routinely measured by variety of instruments. SOLIS/VSM of NSO observes full disk Stokes spectra in photospheric lines which are used to derive vector magnetograms. Hinode SP is a space based spectropolarimeter which has the same observable as SOLIS albeit with limited field-of-view (FOV) but high spatial resolution. SDO/HMI derives vector magnetograms from full disk Stokes measurements, with rather limited spectral resolution, from space in a different photospheric line. Further, these datasets now exist for several years. SOLIS/VSM from 2003, Hinode SP from 2006, and SDO HMI since 2010. Using these time series of vector magnetograms we compute the electric current density in active regions during solar cycle 24 and study the hemispheric distributions. Many studies show that the helicity parameters and proxies show a strong hemispheric bias, such that Northern hemisphere has preferentially negative and southern positive helicity, respectively. We will confirm these results for cycle 24 from three different datasets and evaluate the statistical significance of the hemispheric bias. Further, we discuss the solar cycle variation in the hemispheric helicity pattern during cycle 24 and discuss its implications in terms of solar dynamo models.

Characteristics of chiral plasma plumes generated in the absence of external magnetic field

NASA Astrophysics Data System (ADS)

Nie, LanLan; Liu, FengWu; Zhou, XinCai; Lu, XinPei; Xian, YuBin

2018-05-01

A chiral plasma plume has recently been generated inside a dielectric tube without the use of an external magnetic field. In this paper, we seek to further study the key properties of such a chiral plume to improve our understanding of how this interesting structure is generated and controlled. The chiral plume is generated by externally mounting a stainless steel helical coil or a ring onto the dielectric tube. By changing the pitch of the helical coil, the pitch of the plasma plume can be controlled, with the shape of the plume following the shape of the helical coil. The addition of the helical coil significantly expands the range of parameters under which the chiral plasma plume appears. When the frequency of the applied voltage increases, additional stable discharge channels appear between the adjacent helices. The addition of two helical coils results in the formation of two chiral plasma plumes, which follow the shape of the helical coils. When a metal ring is placed on the outside of the tube, there is no chiral plasma plume between the high voltage electrode and the ring; however, a chiral plasma plume appears on the right side of the ring if the distance between the ring and the high voltage electrode is small. These findings suggest that the chiral plasma can be effectively modulated and guided using an externally mounted helical coil, which acts as the floating/actual ground to reduce the impedance of the discharge and as such contributes to the emergence of the chiral plasma plume behavior.

Ratio of ellipticities between 192 and 208 nm (R1 ): An effective electronic circular dichroism parameter for characterization of the helical components of proteins and peptides.

PubMed

Banerjee, Raja; Sheet, Tridip

2017-11-01

Circular dichroism (CD) spectroscopy represents an important tool for characterization of the peptide and protein secondary structures that mainly arise from the conformational disposition of the peptide backbone in solution. In 1991 Manning and Woody proposed that, in addition to the signal intensity, the ratio between [θ]nπ* and [θ]ππ*ǁ ((R 2 ) ≅ [θ] 222 /[θ] 208 ), along with [θ]ππ*⊥ and [θ]ππ*ǁ ((R 1 ) ≅ [θ] 192 /[θ] 208 ), may be utilized towards identifying the peptide/protein conformation (especially 3 10 - and α-helices). However, till date the use of the ratiometric ellipticity component for helical structure analysis of peptides and proteins has not been reported. We studied a series of temperature dependent CD spectra of a thermally stable, model helical peptide and its related analogs in water as a function of added 2,2,2-trifluoroethanol (TFE) in order to explore their landscape of helicity. For the first time, we have experimentally shown here that the R 1 parameter can characterize better the individual helices, while the other parameter R 2 and the signal intensity do not always converge. We emphasize the use of the R 1 ratio of ellipticities for helical characterization because of the common origin of these two bands (exciton splitting of the amide π→ π* transition in a helical polypeptide). This approach may become worthwhile and timely with the increasing accessibility of CD synchrotron sources. © 2017 Wiley Periodicals, Inc.

Flow through triple helical microchannel

NASA Astrophysics Data System (ADS)

Rajbanshi, Pravat; Ghatak, Animangsu

2018-02-01

Flow through helical tubes and channels have been examined in different contexts, for facilitating heat and mass transfer at low Reynolds number flow, for generating plug flow to minimize reactor volume for many reactions. The curvature and torsion of the helices have been shown to engender secondary flow in addition to the primary axial flow, which enhances passive in-plane mixing between different fluid streams. Most of these studies, however, involve a single spiral with circular cross-section, which in essence is symmetric. It is not known, however, how the coupled effect of asymmetry of cross-section and the curvature and torsion of channel would affect the flow profile inside such tubes or channels. In this context, we have presented here the analysis of fluid flow at low Reynolds number inside a novel triple helical channel that consists of three helical flow paths joined along their contour length forming a single channel. We have carried out both microparticle image velocimetry (micro-PIV) and 3D simulation in FLUENT of flow of a Newtonian fluid through such channels. Our analysis shows that whereas in conventional single helices, the secondary flow is characterized by two counter-rotating vortices, in the case of triple helical channels, number of such vortices increases with the helix angle. Such flow profile is expected to enhance possibility of mixing between the liquids, yet diminish the pressure drop.

Ribbons characterize magnetohydrodynamic magnetic fields better than lines: a lesson from dynamo theory

NASA Astrophysics Data System (ADS)

Blackman, Eric G.; Hubbard, Alexander

2014-08-01

Blackman and Brandenburg argued that magnetic helicity conservation in dynamo theory can in principle be captured by diagrams of mean field dynamos when the magnetic fields are represented by ribbons or tubes, but not by lines. Here, we present such a schematic ribbon diagram for the α2 dynamo that tracks magnetic helicity and provides distinct scales of large-scale magnetic helicity, small-scale magnetic helicity, and kinetic helicity involved in the process. This also motivates our construction of a new `2.5 scale' minimalist generalization of the helicity-evolving equations for the α2 dynamo that separately allows for these three distinct length-scales while keeping only two dynamical equations. We solve these equations and, as in previous studies, find that the large-scale field first grows at a rate independent of the magnetic Reynolds number RM before quenching to an RM-dependent regime. But we also show that the larger the ratio of the wavenumber where the small-scale current helicity resides to that of the forcing scale, the earlier the non-linear dynamo quenching occurs, and the weaker the large-scale field is at the turnoff from linear growth. The harmony between the theory and the schematic diagram exemplifies a general lesson that magnetic fields in magnetohydrodynamic are better visualized as two-dimensional ribbons (or pairs of lines) rather than single lines.

The biomechanical role of overall-shape transformation in a primitive multicellular organism: A case study of dimorphism in the filamentous cyanobacterium Arthrospira platensis.

PubMed

Chaiyasitdhi, Atitheb; Miphonpanyatawichok, Wirat; Riehle, Mathis Oliver; Phatthanakun, Rungrueang; Surareungchai, Werasak; Kundhikanjana, Worasom; Kuntanawat, Panwong

2018-01-01

Morphological transformations in primitive organisms have long been observed; however, its biomechanical roles are largely unexplored. In this study, we investigate the structural advantages of dimorphism in Arthrospira platensis, a filamentous multicellular cyanobacterium. We report that helical trichomes, the default shape, have a higher persistence length (Lp), indicating a higher resistance to bending or a large value of flexural rigidity (kf), the product of the local cell stiffness (E) and the moment of inertia of the trichomes' cross-section (I). Through Atomic Force Microscopy (AFM), we determined that the E of straight and helical trichomes were the same. In contrast, our computational model shows that I is greatly dependent on helical radii, implying that trichome morphology is the major contributor to kf variation. According to our estimation, increasing the helical radii alone can increase kf by 2 orders of magnitude. We also observe that straight trichomes have improved gliding ability, due to its structure and lower kf. Our study shows that dimorphism provides mechanical adjustability to the organism and may allow it to thrive in different environmental conditions. The higher kf provides helical trichomes a better nutrient uptake through advection in aquatic environments. On the other hand, the lower kf improves the gliding ability of straight trichomes in aquatic environments, enabling it to chemotactically relocate to more favorable territories when it encounters certain environmental stresses. When more optimal conditions are encountered, straight trichomes can revert to their original helical form. Our study is one of the first to highlight the biomechanical role of an overall-shape transformation in cyanobacteria.

Point-source helicity injection for ST plasma startup in Pegasus

NASA Astrophysics Data System (ADS)

Redd, A. J.; Battaglia, D. J.; Bongard, M. W.; Fonck, R. J.; Schlossberg, D. J.

2009-11-01

Plasma current guns are used as point-source DC helicity injectors for forming non-solenoidal tokamak plasmas in the Pegasus Toroidal Experiment. Discharges driven by this injection scheme have achieved Ip>= 100 kA using Iinj<= 4 kA. They form at the outboard midplane, transition to a tokamak-like equilibrium, and continue to grow inward as Ip increases due to helicity injection and outer- PF induction. The maximum Ip is determined by helicity balance (injection rate vs resistive dissipation) and a Taylor relaxation limit, in which Ip√ITF Iinj/w, where w is the radial thickness of the gun-driven edge. Preliminary experiments tentatively confirm these scalings with ITF, Iinj, and w, increasing confidence in this simple relaxation model. Adding solenoidal inductive drive during helicity injection can push Ip up to, but not beyond, the predicted relaxation limit, demonstrating that this is a hard performance limit. Present experiments are focused on increasing the injection voltage (i.e., helicity injection rate) and reducing w. Near-term goals are to further test scalings predicted by the simple relaxation model and to study in detail the observed bursty n=1 activity correlated with rapid increases in Ip.

The influence of the aortic valve angle on the hemodynamic features of the thoracic aorta

NASA Astrophysics Data System (ADS)

Ha, Hojin; Kim, Guk Bae; Kweon, Jihoon; Lee, Sang Joon; Kim, Young-Hak; Kim, Namkug; Yang, Dong Hyun

2016-08-01

Since the first observation of a helical flow pattern in aortic blood flow, the existence of helical blood flow has been found to be associated with various pathological conditions such as bicuspid aortic valve, aortic stenosis, and aortic dilatation. However, an understanding of the development of helical blood flow and its clinical implications are still lacking. In our present study, we hypothesized that the direction and angle of aortic inflow can influence helical flow patterns and related hemodynamic features in the thoracic aorta. Therefore, we investigated the hemodynamic features in the thoracic aorta and various aortic inflow angles using patient-specific vascular phantoms that were generated using a 3D printer and time-resolved, 3D, phase-contrast magnetic resonance imaging (PC-MRI). The results show that the rotational direction and strength of helical blood flow in the thoracic aorta largely vary according to the inflow direction of the aorta, and a higher helical velocity results in higher wall shear stress distributions. In addition, right-handed rotational flow conditions with higher rotational velocities imply a larger total kinetic energy than left-handed rotational flow conditions with lower rotational velocities.

The influence of the aortic valve angle on the hemodynamic features of the thoracic aorta.

PubMed

Ha, Hojin; Kim, Guk Bae; Kweon, Jihoon; Lee, Sang Joon; Kim, Young-Hak; Kim, Namkug; Yang, Dong Hyun

2016-08-26

Since the first observation of a helical flow pattern in aortic blood flow, the existence of helical blood flow has been found to be associated with various pathological conditions such as bicuspid aortic valve, aortic stenosis, and aortic dilatation. However, an understanding of the development of helical blood flow and its clinical implications are still lacking. In our present study, we hypothesized that the direction and angle of aortic inflow can influence helical flow patterns and related hemodynamic features in the thoracic aorta. Therefore, we investigated the hemodynamic features in the thoracic aorta and various aortic inflow angles using patient-specific vascular phantoms that were generated using a 3D printer and time-resolved, 3D, phase-contrast magnetic resonance imaging (PC-MRI). The results show that the rotational direction and strength of helical blood flow in the thoracic aorta largely vary according to the inflow direction of the aorta, and a higher helical velocity results in higher wall shear stress distributions. In addition, right-handed rotational flow conditions with higher rotational velocities imply a larger total kinetic energy than left-handed rotational flow conditions with lower rotational velocities.

The influence of the aortic valve angle on the hemodynamic features of the thoracic aorta

PubMed Central

Ha, Hojin; Kim, Guk Bae; Kweon, Jihoon; Lee, Sang Joon; Kim, Young-Hak; Kim, Namkug; Yang, Dong Hyun

2016-01-01

Since the first observation of a helical flow pattern in aortic blood flow, the existence of helical blood flow has been found to be associated with various pathological conditions such as bicuspid aortic valve, aortic stenosis, and aortic dilatation. However, an understanding of the development of helical blood flow and its clinical implications are still lacking. In our present study, we hypothesized that the direction and angle of aortic inflow can influence helical flow patterns and related hemodynamic features in the thoracic aorta. Therefore, we investigated the hemodynamic features in the thoracic aorta and various aortic inflow angles using patient-specific vascular phantoms that were generated using a 3D printer and time-resolved, 3D, phase-contrast magnetic resonance imaging (PC-MRI). The results show that the rotational direction and strength of helical blood flow in the thoracic aorta largely vary according to the inflow direction of the aorta, and a higher helical velocity results in higher wall shear stress distributions. In addition, right-handed rotational flow conditions with higher rotational velocities imply a larger total kinetic energy than left-handed rotational flow conditions with lower rotational velocities. PMID:27561388

Velocity Fluctuations in Helical Propulsion: How Small Can a Propeller Be.

PubMed

Ghosh, Arijit; Paria, Debadrita; Rangarajan, Govindan; Ghosh, Ambarish

2014-01-02

Helical propulsion is at the heart of locomotion strategies utilized by various natural and artificial swimmers. We used experimental observations and a numerical model to study the various fluctuation mechanisms that determine the performance of an externally driven helical propeller as the size of the helix is reduced. From causality analysis, an overwhelming effect of orientational noise at low length scales is observed, which strongly affects the average velocity and direction of motion of a propeller. For length scales smaller than a few micrometers in aqueous media, the operational frequency for the propulsion system would have to increase as the inverse cube of the size, which can be the limiting factor for a helical propeller to achieve locomotion in the desired direction.

Dynamo transition in low-dimensional models.

PubMed

Verma, Mahendra K; Lessinnes, Thomas; Carati, Daniele; Sarris, Ioannis; Kumar, Krishna; Singh, Meenakshi

2008-09-01

Two low-dimensional magnetohydrodynamic models containing three velocity and three magnetic modes are described. One of them (nonhelical model) has zero kinetic and current helicity, while the other model (helical) has nonzero kinetic and current helicity. The velocity modes are forced in both these models. These low-dimensional models exhibit a dynamo transition at a critical forcing amplitude that depends on the Prandtl number. In the nonhelical model, dynamo exists only for magnetic Prandtl number beyond 1, while the helical model exhibits dynamo for all magnetic Prandtl number. Although the model is far from reproducing all the possible features of dynamo mechanisms, its simplicity allows a very detailed study and the observed dynamo transition is shown to bear similarities with recent numerical and experimental results.

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.

Right-Handed Helical Foldamers Consisting of De Novo d -AApeptides

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

Teng, Peng; Ma, Ning; Cerrato, Darrell Cole

New types of foldamer scaffolds are formidably challenging to design and synthesize, yet highly desirable as structural mimics of peptides/proteins with a wide repertoire of functions. In particular, the development of peptidomimetic helical foldamers holds promise for new biomaterials, catalysts, and drug molecules. Unnatural l-sulfono-γ-AApeptides were recently developed and shown to have potential applications in both biomedical and material sciences. However, d-sulfono-γ-AApeptides, the enantiomers of l-sulfono-γ-AApeptides, have never been studied due to the lack of high-resolution three-dimensional structures to guide structure-based design. Herein, we report the first synthesis and X-ray crystal structures of a series of 2:1 l-amino acid/d-sulfono-γ-AApeptide hybridmore » foldamers, and elucidate their folded conformation at the atomic level. Single-crystal X-ray crystallography indicates that this class of oligomers folds into well-defined right-handed helices with unique helical parameters. The helical structures were consistent with data obtained from solution 2D NMR, CD studies, and molecular dynamics simulations. Our findings are expected to inspire the structure-based design of this type of unique folding biopolymers for biomaterials and biomedical applications.« 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

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

Arachidonic acid mediates the formation of abundant alpha-helical multimers of alpha-synuclein

NASA Astrophysics Data System (ADS)

Iljina, Marija; Tosatto, Laura; Choi, Minee L.; Sang, Jason C.; Ye, Yu; Hughes, Craig D.; Bryant, Clare E.; Gandhi, Sonia; Klenerman, David

2016-09-01

The protein alpha-synuclein (αS) self-assembles into toxic beta-sheet aggregates in Parkinson’s disease, while it is proposed that αS forms soluble alpha-helical multimers in healthy neurons. Here, we have made αS multimers in vitro using arachidonic acid (ARA), one of the most abundant fatty acids in the brain, and characterized them by a combination of bulk experiments and single-molecule Fӧrster resonance energy transfer (sm-FRET) measurements. The data suggest that ARA-induced oligomers are alpha-helical, resistant to fibril formation, more prone to disaggregation, enzymatic digestion and degradation by the 26S proteasome, and lead to lower neuronal damage and reduced activation of microglia compared to the oligomers formed in the absence of ARA. These multimers can be formed at physiologically-relevant concentrations, and pathological mutants of αS form less multimers than wild-type αS. Our work provides strong biophysical evidence for the formation of alpha-helical multimers of αS in the presence of a biologically relevant fatty acid, which may have a protective role with respect to the generation of beta-sheet toxic structures during αS fibrillation.

Compositionally-graded silicon-copper helical arrays as anodes for lithium-ion batteries

NASA Astrophysics Data System (ADS)

Polat, Deniz B.; Keles, Ozgul; Amine, Khalil

2016-02-01

Restrictions in silicon based anodes have been the subject of many researches for years. As an innovative approach, we have adopted ion assisted deposition technique to glancing angle deposition method and have used compositionally-graded structuring. A unique helical shaped gradient film has been produced in which the Cu/Si atomic ratio decreases from the bottom to the top of the coating. With such a unique film (high surface area) more spaces have been created promoting mechanical integrity and reaction between active materials (silicon) with lithium ions. The highly adherent film is formed as a result of ion assisted deposition process and the gradual change in Cu/Si atomic ratio diverts stress through the helices. To compare the performance of the SiCu electrode, a pure Si film is deposited in the same experimental condition. Galvanostatic test results show that although the film with pure Si helices fails after 30th cycles, the compositionally graded anode exhibits a capacity of 1228 mAh g-1 at the 100th cycles with 99.5% coulombic efficiencies when cycled at 100 mA g-1, and delivers 815 mAh g-1 when cycled with a rate of 400 mA g-1.

Distributed temperature sensors development using an stepped-helical ultrasonic waveguide

NASA Astrophysics Data System (ADS)

Periyannan, Suresh; Rajagopal, Prabhu; Balasubramaniam, Krishnan

2018-04-01

This paper presents the design and development of the distributed ultrasonic waveguide temperature sensors using some stepped-helical structures. Distributed sensing has several applications in various industries (oil, glass, steel) for measurement of physical parameters such as level, temperature, viscosity, etc. This waveguide incorporates a special notch or bend for obtaining ultrasonic wave reflections from the desired locations (Gage-lengths) where local measurements are desired. In this paper, a multi-location measurement wave-guide, with a measurement capability of 18 locations in a single wire, has been fabricated. The distribution of these sensors is both in the axial as well as radial directions using a stepped-helical spring configuration. Also, different high temperature materials have been chosen for the wave-guide. Both lower order axi-symmetric guided ultrasonic modes (L(0,1) and T(0,1)) were employed. These wave modes were generated/received (pulse-echo approach) using conventional longitudinal and shear transducers, respectively. Also, both the wave modes were simultaneously generated/received and compared using shear transducer for developing the distributed helical wave-guide sensors. The effect of dispersion of the wave modes due to curvature effects will also be discussed.

Four highly pseudosymmetric and/or twinned structures of d(CGCGCG) 2 extend the repertoire of crystal structures of Z-DNA

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

Luo, Zhipu; Dauter, Zbigniew; Gilski, Miroslaw

DNA oligomer duplexes containing alternating cytosines and guanines in their sequences tend to form left-handed helices of the Z-DNA type, with the sugar and phosphate backbone in a zigzag conformation and a helical repeat of two successive nucleotides. Z-DNA duplexes usually crystallize as hexagonally arranged parallel helical tubes, with various relative orientations and translation of neighboring duplexes. Four novel high-resolution crystal structures of d(CGCGCG) 2duplexes are described here. They are characterized by a high degree of pseudosymmetry and/or twinning, with three or four independent duplexes differently oriented in a monoclinicP2 1lattice of hexagonal metric. The various twinning criteria give somewhatmore » conflicting indications in these complicated cases of crystal pathology. The details of molecular packing in these crystal structures are compared with other known crystal forms of Z-DNA.« less

Steady-state helices of the actin homolog MreB inside bacteria: dynamics without motors.

PubMed

Allard, Jun F; Rutenberg, Andrew D

2007-09-01

Within individual bacteria, we combine force-dependent polymerization dynamics of individual MreB protofilaments with an elastic model of protofilament bundles buckled into helical configurations. We use variational techniques and stochastic simulations to relate the pitch of the MreB helix, the total abundance of MreB, and the number of protofilaments. By comparing our simulations with mean-field calculations, we find that stochastic fluctuations are significant. We examine the quasistatic evolution of the helical pitch with cell growth, as well as time scales of helix turnover and de novo establishment. We find that while the body of a polarized MreB helix treadmills toward its slow-growing end, the fast-growing tips of laterally associated protofilaments move toward the opposite fast-growing end of the MreB helix. This offers a possible mechanism for targeted polar localization without cytoplasmic motor proteins.

Steady-state helices of the actin homolog MreB inside bacteria: Dynamics without motors

NASA Astrophysics Data System (ADS)

Allard, Jun F.; Rutenberg, Andrew D.

2007-09-01

Within individual bacteria, we combine force-dependent polymerization dynamics of individual MreB protofilaments with an elastic model of protofilament bundles buckled into helical configurations. We use variational techniques and stochastic simulations to relate the pitch of the MreB helix, the total abundance of MreB, and the number of protofilaments. By comparing our simulations with mean-field calculations, we find that stochastic fluctuations are significant. We examine the quasistatic evolution of the helical pitch with cell growth, as well as time scales of helix turnover and de novo establishment. We find that while the body of a polarized MreB helix treadmills toward its slow-growing end, the fast-growing tips of laterally associated protofilaments move toward the opposite fast-growing end of the MreB helix. This offers a possible mechanism for targeted polar localization without cytoplasmic motor proteins.

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

PubMed

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

2016-01-11

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

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.

An Amino Acid Packing Code for α-helical Structure and Protein Design

PubMed Central

Joo, Hyun; Chavan, Archana G.; Phan, Jamie; Day, Ryan; Tsai, Jerry

2012-01-01

This work demonstrates that all packing in α-helices can be simplified to repetitive patterns of a single motif: the knob-socket. Using the precision of Voronoi Polyhedra/Deluaney Tessellations to identify contacts, the knob-socket is a 4 residue tetrahedral motif: a knob residue on one α-helix packs into the 3 residue socket on another α-helix. The principle of the knob-socket model relates the packing between levels of protein structure: the intra-helical packing arrangements within secondary structure that permit inter-helix tertiary packing interactions. Within an α-helix, the 3 residue sockets arrange residues into a uniform packing lattice. Inter-helix packing results from a definable pattern of interdigitated knob-socket motifs between 2 α-helices. Furthermore, the knob-socket model classifies 3 types of sockets: 1) free: favoring only intra-helical packing, 2) filled: favoring inter-helical interactions and 3) non: disfavoring α-helical structure. The amino acid propensities in these 3 socket classes essentially represent an amino acid code for structure in α-helical packing. Using this code, a novel yet straightforward approach for the design of α-helical structure was used to validate the knob-socket model. Unique sequences for 3 peptides were created to produce a predicted amount of α-helical structure: mostly helical, some helical, and no-helix. These 3 peptides were synthesized and helical content assessed using CD spectroscopy. The measured α-helicity of each peptide was consistent with the expected predictions. These results and analysis demonstrate that the knob-socket motif functions as the basic unit of packing and presents an intuitive tool to decipher the rules governing packing in protein structure. PMID:22426125

Mechanics of tunable helices and geometric frustration in biomimetic seashells

NASA Astrophysics Data System (ADS)

Guo, Qiaohang; Chen, Zi; Li, Wei; Dai, Pinqiang; Ren, Kun; Lin, Junjie; Taber, Larry A.; Chen, Wenzhe

2014-03-01

Helical structures are ubiquitous in nature and engineering, ranging from DNA molecules to plant tendrils, from sea snail shells to nanoribbons. While the helical shapes in natural and engineered systems often exhibit nearly uniform radius and pitch, helical shell structures with changing radius and pitch, such as seashells and some plant tendrils, add to the variety of this family of aesthetic beauty. Here we develop a comprehensive theoretical framework for tunable helical morphologies, and report the first biomimetic seashell-like structure resulting from mechanics of geometric frustration. In previous studies, the total potential energy is everywhere minimized when the system achieves equilibrium. In this work, however, the local energy minimization cannot be realized because of the geometric incompatibility, and hence the whole system deforms into a shape with a global energy minimum whereby the energy in each segment may not necessarily be locally optimized. This novel approach can be applied to develop materials and devices of tunable geometries with a range of applications in nano/biotechnology.

Unfolding four-helix bundles

NASA Astrophysics Data System (ADS)

Gray, Harry B.; Winkler, Jay R.; Kozak, John J.

2011-03-01

A geometrical model has been developed to describe the early stages of unfolding of cytochromes c‧ and c-b562 . Calculations are based on a step-wise extension of the polypeptide chain subject to the constraint that the spatial relationship among the residues of each triplet is fixed by the native-state crystallographic data. The response of each protein to these structural perturbations allows the evolution of each of the four helices in these two proteins to be differentiated. It is found that the two external helices in c‧ unfold before its two internal helices, whereas exactly the opposite behaviour is demonstrated by c-b562 . Each of these cytochromes has an extended, internal, non-helical ('turning') region that initially lags behind the most labile helix but then, at a certain stage (identified for each cytochrome), unravels before any of the four helices present in the native structure. It is believed that these predictions will be useful in guiding future experimental studies on the unfolding of these two cytochromes.

TMSEG: Novel prediction of transmembrane helices.

PubMed

Bernhofer, Michael; Kloppmann, Edda; Reeb, Jonas; Rost, Burkhard

2016-11-01

Transmembrane proteins (TMPs) are important drug targets because they are essential for signaling, regulation, and transport. Despite important breakthroughs, experimental structure determination remains challenging for TMPs. Various methods have bridged the gap by predicting transmembrane helices (TMHs), but room for improvement remains. Here, we present TMSEG, a novel method identifying TMPs and accurately predicting their TMHs and their topology. The method combines machine learning with empirical filters. Testing it on a non-redundant dataset of 41 TMPs and 285 soluble proteins, and applying strict performance measures, TMSEG outperformed the state-of-the-art in our hands. TMSEG correctly distinguished helical TMPs from other proteins with a sensitivity of 98 ± 2% and a false positive rate as low as 3 ± 1%. Individual TMHs were predicted with a precision of 87 ± 3% and recall of 84 ± 3%. Furthermore, in 63 ± 6% of helical TMPs the placement of all TMHs and their inside/outside topology was correctly predicted. There are two main features that distinguish TMSEG from other methods. First, the errors in finding all helical TMPs in an organism are significantly reduced. For example, in human this leads to 200 and 1600 fewer misclassifications compared to the second and third best method available, and 4400 fewer mistakes than by a simple hydrophobicity-based method. Second, TMSEG provides an add-on improvement for any existing method to benefit from. Proteins 2016; 84:1706-1716. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

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.

Stabilization of Helivcal Order in the Thick Filaments by Blebbistatin: Further Evidence of Coexisting Multiple Conformations of Myosin

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

Xu, S.; White, H; Offer, G

2009-01-01

The degree of helical order of the thick filament of mammalian skeletal muscle is highly dependent on temperature and the nature of the ligand. Previously, we showed that there was a close correlation between the conformation of the myosin heads on the surface of the thick filaments and the extent of their helical order. Helical order required the heads to be in the closed conformation. In addition, we showed that, with the same ligand bound at the active site, three conformations of myosin coexisted in equilibrium. Hitherto, however, there was no detectable helical order as measured by x-ray diffraction undermore » the temperatures studied for myosin with MgADP and the nucleotide-free myosin, raising the possibility that the concept of multiple conformations has limited validity. In this study, blebbistatin was used to stabilize the closed conformation of myosin. The degree of helical order is substantially improved with MgATP at low temperature or with MgADP or in the absence of nucleotide. The thermodynamic parameters of the disorder?order transition and the characteristics of the ordered array were not significantly altered by binding blebbistatin. The simplest explanation is that the binding of blebbistatin increases the proportion of myosin in the closed conformation from being negligible to substantial. These results provide further evidence for the coexistence of multiple conformations of myosin under a wide range of conditions and for the closed conformation being directly coupled to helical order.« less

RELATIONSHIPS BETWEEN FLUID VORTICITY, KINETIC HELICITY, AND MAGNETIC FIELD ON SMALL-SCALES (QUIET-NETWORK) ON THE SUN

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

Sangeetha, C. R.; Rajaguru, S. P., E-mail: crsangeetha@iiap.res.in

We derive horizontal fluid motions on the solar surface over large areas covering the quiet-Sun magnetic network from local correlation tracking of convective granules imaged in continuum intensity and Doppler velocity by the Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory . From these we calculate the horizontal divergence, the vertical component of vorticity, and the kinetic helicity of fluid motions. We study the correlations between fluid divergence and vorticity, and between vorticity (kinetic helicity) and the magnetic field. We find that the vorticity (kinetic helicity) around small-scale fields exhibits a hemispherical pattern (in sign) similar tomore » that followed by the magnetic helicity of large-scale active regions (containing sunspots). We identify this pattern to be a result of the Coriolis force acting on supergranular-scale flows (both the outflows and inflows), consistent with earlier studies using local helioseismology. Furthermore, we show that the magnetic fields cause transfer of vorticity from supergranular inflow regions to outflow regions, and that they tend to suppress the vortical motions around them when magnetic flux densities exceed about 300 G (from HMI). We also show that such an action of the magnetic fields leads to marked changes in the correlations between fluid divergence and vorticity. These results are speculated to be of importance to local dynamo action (if present) and to the dynamical evolution of magnetic helicity at the small-scale.« less

Stability of the Helical TomoTherapy Hi·Art II detector for treatment beam irradiations

PubMed Central

Schombourg, Karin; Bochud, François

2014-01-01

The Hi·Art II Helical TomoTherapy (HT) unit is equipped with a built‐in onboard MVCT detector used for patient imaging and beam monitoring. Our aim was to study the detector stability for treatment beam measurements. We studied the MVCT detector response with the 6 MV photon beam over time, throughout short‐term (during an irradiation) and long‐term (two times 50 days) periods. Our results show a coefficient of variation ≤1% for detector chambers inside the beam (excluding beam gradients) for short‐ and long‐term response of the MVCT detector. Larger variations were observed in beam gradients and an influence of the X‐ray target where degradation was found. The results assume that an ‘air scan’ procedure is performed daily to recalibrate the detector with the imaging beam. On short term, the detector response stability is comparable to other devices. Long‐term measurements during two 50‐day periods show a good reproducibility. PACS numbers: 87.55.ne, 87.55.Qr PMID:25493514

Changes in type I collagen following laser welding.

PubMed

Bass, L S; Moazami, N; Pocsidio, J; Oz, M C; LoGerfo, P; Treat, M R

1992-01-01

Selection of ideal laser parameters for tissue welding is inhibited by poor understanding of the mechanism. We investigated structural changes in collagen molecules extracted from rat tail tendon (> 90% type I collagen) after tissue welding using an 808 nm diode laser and indocyanine green dye applied to the weld site. Mobility patterns on SDS-PAGE were identical in the lasered and untreated tendon extracts with urea or acetic acid. Pepsin incubation after acetic acid extraction revealed a reduction of collagen alpha and beta bands in lasered compared with untreated specimens. Circular dichroism studies of rat tail tendon showed absence of helical structure in collagen from lasered tendon. No evidence for covalent bonding was present in laser-treated tissues. Collagen molecules are denatured by the laser wavelength and parameters used in this study. No significant amount of helical structure is regenerated on cooling. We conclude that non-covalent interactions between denatured collagen molecules may be responsible for the creation of tissue welding.

In silico studies of the properties of water hydrating a small protein

NASA Astrophysics Data System (ADS)

Sinha, Sudipta Kumar; Jana, Madhurima; Chakraborty, Kausik; Bandyopadhyay, Sanjoy

2014-12-01

Atomistic molecular dynamics simulation of an aqueous solution of the small protein HP-36 has been carried out with explicit solvent at room temperature. Efforts have been made to explore the influence of the protein on the relative packing and ordering of water molecules around its secondary structures, namely, three α-helices. The calculations reveal that the inhomogeneous water ordering and density distributions around the helices are correlated with their relative hydrophobicity. Importantly, we have identified the existence of a narrow relatively dehydrated region containing randomly organized "quasi-free" water molecules beyond the first layer of "bound" waters at the protein surface. These water molecules with relatively weaker binding energies form the transition state separating the "bound" and "free" water molecules at the interface. Further, increased contribution of solid-like caging motions of water molecules around the protein is found to be responsible for reduced fluidity of the hydration layer. Interestingly, we notice that the hydration layer of helix-3 is more fluidic with relatively higher entropy as compared to the hydration layers of the other two helical segments. Such characteristics of helix-3 hydration layer correlate well with the activity of HP-36, as helix-3 contains the active site of the protein.

Extending Three-Dimensional Weighted Cone Beam Filtered Backprojection (CB-FBP) Algorithm for Image Reconstruction in Volumetric CT at Low Helical Pitches

PubMed Central

Hsieh, Jiang; Nilsen, Roy A.; McOlash, Scott M.

2006-01-01

A three-dimensional (3D) weighted helical cone beam filtered backprojection (CB-FBP) algorithm (namely, original 3D weighted helical CB-FBP algorithm) has already been proposed to reconstruct images from the projection data acquired along a helical trajectory in angular ranges up to [0, 2 π]. However, an overscan is usually employed in the clinic to reconstruct tomographic images with superior noise characteristics at the most challenging anatomic structures, such as head and spine, extremity imaging, and CT angiography as well. To obtain the most achievable noise characteristics or dose efficiency in a helical overscan, we extended the 3D weighted helical CB-FBP algorithm to handle helical pitches that are smaller than 1: 1 (namely extended 3D weighted helical CB-FBP algorithm). By decomposing a helical over scan with an angular range of [0, 2π + Δβ] into a union of full scans corresponding to an angular range of [0, 2π], the extended 3D weighted function is a summation of all 3D weighting functions corresponding to each full scan. An experimental evaluation shows that the extended 3D weighted helical CB-FBP algorithm can improve noise characteristics or dose efficiency of the 3D weighted helical CB-FBP algorithm at a helical pitch smaller than 1: 1, while its reconstruction accuracy and computational efficiency are maintained. It is believed that, such an efficient CB reconstruction algorithm that can provide superior noise characteristics or dose efficiency at low helical pitches may find its extensive applications in CT medical imaging. PMID:23165031

Characterization of paired helical filaments by scanning transmission electron microscopy.

PubMed

Ksiezak-Reding, Hanna; Wall, Joseph S

2005-07-01

Paired helical filaments (PHFs) are abnormal twisted filaments composed of hyperphosphorylated tau protein. They are found in Alzheimer's disease and other neurodegenerative disorders designated as tauopathies. They are a major component of intracellular inclusions known as neurofibrillary tangles (NFTs). The objective of this review is to summarize various structural studies of PHFs in which using scanning transmission electron microscopy (STEM) has been particularly informative. STEM provides shape and mass per unit length measurements important for studying ultrastructural aspects of filaments. These include quantitative comparisons between dispersed and aggregated populations of PHFs as well as comparative studies of PHFs in Alzheimer's disease and other neurodegenerative disorders. Other approaches are also discussed if relevant or complementary to studies using STEM, e.g., application of a novel staining reagent, Nanovan. Our understanding of the PHF structure and the development of PHFs into NFTs is presented from a historical perspective. Others goals are to describe the biochemical and ultrastructural complexity of authentic PHFs, to assess similarities between authentic and synthetic PHFs, and to discuss recent advances in PHF modeling.

On Three-dimensional Structures in Relativistic Hydrodynamic Jets

NASA Astrophysics Data System (ADS)

Hardee, Philip E.

2000-04-01

The appearance of wavelike helical structures on steady relativistic jets is studied using a normal mode analysis of the linearized fluid equations. Helical structures produced by the normal modes scale relative to the resonant (most unstable) wavelength and not with the absolute wavelength. The resonant wavelength of the normal modes can be less than the jet radius even on highly relativistic jets. High-pressure regions helically twisted around the jet beam may be confined close to the jet surface, penetrate deeply into the jet interior, or be confined to the jet interior. The high-pressure regions range from thin and ribbon-like to thick and tubelike depending on the mode and wavelength. The wave speeds can be significantly different at different wavelengths but are less than the flow speed. The highest wave speed for the jets studied has a Lorentz factor somewhat more than half that of the underlying flow speed. A maximum pressure fluctuation criterion found through comparison between theory and a set of relativistic axisymmetric jet simulations is applied to estimate the maximum amplitudes of the helical, elliptical, and triangular normal modes. Transverse velocity fluctuations for these asymmetric modes are up to twice the amplitude of those associated with the axisymmetric pinch mode. The maximum amplitude of jet distortions and the accompanying velocity fluctuations at, for example, the resonant wavelength decreases as the Lorentz factor increases. Long-wavelength helical surface mode and shorter wavelength helical first body mode generated structures should be the most significant. Emission from high-pressure regions as they twist around the jet beam can vary significantly as a result of angular variation in the flow direction associated with normal mode structures if they are viewed at about the beaming angle θ=1/γ. Variation in the Doppler boost factor can lead to brightness asymmetries by factors up to 6 as long-wavelength helical structure produced by the helical surface mode winds around the jet. Higher order surface modes and first body modes produce less variation. Angular variation in the flow direction associated with the helical mode appears consistent with precessing jet models that have been proposed to explain the variability in 3C 273 and BL Lac object AO 0235+164. In particular, cyclic angular variation in the flow direction produced by the normal modes could produce the activity seen in BL Lac object OJ 287. Jet precession provides a mechanism for triggering the helical modes on multiple length scales, e.g., the galactic superluminal GRO J1655-40.

Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction.

PubMed

Fromm, S A; Sachse, C

2016-01-01

Treating helices as single-particle-like segments followed by helical image reconstruction has become the method of choice for high-resolution structure determination of well-ordered helical viruses as well as flexible filaments. In this review, we will illustrate how the combination of latest hardware developments with optimized image processing routines have led to a series of near-atomic resolution structures of helical assemblies. Originally, the treatment of helices as a sequence of segments followed by Fourier-Bessel reconstruction revealed the potential to determine near-atomic resolution structures from helical specimens. In the meantime, real-space image processing of helices in a stack of single particles was developed and enabled the structure determination of specimens that resisted classical Fourier helical reconstruction and also facilitated high-resolution structure determination. Despite the progress in real-space analysis, the combination of Fourier and real-space processing is still commonly used to better estimate the symmetry parameters as the imposition of the correct helical symmetry is essential for high-resolution structure determination. Recent hardware advancement by the introduction of direct electron detectors has significantly enhanced the image quality and together with improved image processing procedures has made segmented helical reconstruction a very productive cryo-EM structure determination method. © 2016 Elsevier Inc. All rights reserved.

Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes

PubMed Central

Karch, Rudolf; Schreiner, Wolfgang

2015-01-01

MHC α-helices form the antigen-binding cleft and are of particular interest for immunological reactions. To monitor these helices in molecular dynamics simulations, we applied a parsimonious fragment-fitting method to trace the axes of the α-helices. Each resulting axis was fitted by polynomials in a least-squares sense and the curvature integral was computed. To find the appropriate polynomial degree, the method was tested on two artificially modelled helices, one performing a bending movement and another a hinge movement. We found that second-order polynomials retrieve predefined parameters of helical motion with minimal relative error. From MD simulations we selected those parts of α-helices that were stable and also close to the TCR/MHC interface. We monitored the curvature integral, generated a ruled surface between the two MHC α-helices, and computed interhelical area and surface torsion, as they changed over time. We found that MHC α-helices undergo rapid but small changes in conformation. The curvature integral of helices proved to be a sensitive measure, which was closely related to changes in shape over time as confirmed by RMSD analysis. We speculate that small changes in the conformation of individual MHC α-helices are part of the intrinsic dynamics induced by engagement with the TCR. PMID:26649324

In vivo mechanical study of helical cardiac pacing electrode interacting with canine myocardium

NASA Astrophysics Data System (ADS)

Zhang, Xiangming; Ma, Nianke; Fan, Hualin; Niu, Guodong; Yang, Wei

2007-06-01

Cardiac pacing is a medical device to help human to overcome arrhythmia and to recover the regular beats of heart. A helical configuration of electrode tip is a new type of cardiac pacing lead distal tip. The helical electrode attaches itself to the desired site of heart by screwing its helical tip into the myocardium. In vivo experiments on anesthetized dogs were carried out to measure the acute interactions between helical electrode and myocardium during screw-in and pull-out processes. These data would be helpful for electrode tip design and electrode/myocardium adherence safety evaluation. They also provide reliability data for clinical site choice of human heart to implant and to fix the pacing lead. A special design of the helical tip using strain gauges is instrumented for the measurement of the screw-in and pull-out forces. We obtained the data of screw-in torques and pull-out forces for five different types of helical electrodes at nine designed sites on ten canine hearts. The results indicate that the screw-in torques increased steplike while the torque time curves presente saw-tooth fashion. The maximum torque has a range of 0.3 1.9 N mm. Obvious differences are observed for different types of helical tips and for different test sites. Large pull-out forces are frequently obtained at epicardium of left ventricle and right ventricle lateral wall, and the forces obtained at right ventricle apex and outflow tract of right ventricle are normally small. The differences in pull-out forces are dictated by the geometrical configuration of helix and regional structures of heart muscle.

Radio emission from RS CVn binaries. II - Polarization and spectral properties

NASA Technical Reports Server (NTRS)

Mutel, R. L.; Morris, D. H.; Doiron, D. J.; Lestrade, J. F.

1987-01-01

Multiepoch radio observations of circular polarization and spectral characteristics of several close, late-type stellar binaries are reported. The median luminosity of four well-studied systems ranged from 16.2 to 17.1 ergs/s/Hz. For individual systems, the fractional circular polarization decreases with increasing luminosity, particularly at frequencies above 5 GHz. Eclipsing binaries have significantly lower average circular polarization compared with noneclipsing systems. Helicity reversal is almost always observed between 1.4 and 4.9 GHz for systems with high orbital inclination. Comparison with ten years of previously published polarization observations for two RS CVn stellar systems show that the same helicity occurs at a given frequency for a given source, indicating a very stable, large-scale magnetic field geometry. These spectral and polarization characteristics strongly support a model of inhomogeneous gyrosynchrotron emission arising from electrons with power law energy spectra interacting with inhomogeneous magnetic fields.

Comparison of confinement in resistive-shell reversed-field pinch devices with two different magnetic shell penetration times

NASA Astrophysics Data System (ADS)

Gravestijn, R. M.; Drake, J. R.; Hedqvist, A.; Rachlew, E.

2004-01-01

A loop voltage is required to sustain the reversed-field pinch (RFP) equilibrium. The configuration is characterized by redistribution of magnetic helicity but with the condition that the total helicity is maintained constant. The magnetic field shell penetration time, tgrs, has a critical role in the stability and performance of the RFP. Confinement in the EXTRAP device has been studied with two values of tgrs, first (EXTRAP-T2) with tgrs of the order of the typical relaxation cycle timescale and then (EXTRAP-T2R) with tgrs much longer than the relaxation cycle timescale, but still much shorter than the pulse length. Plasma parameters show significant improvements in confinement in EXTRAP-T2R. The typical loop voltage required to sustain comparable electron poloidal beta values is a factor of 3 lower in the EXTRAP-T2R device. The improvement is attributed to reduced magnetic turbulence.

Synergistic Enhancement of Microwave Absorption Using Hybridized Polyaniline@helical CNTs with Dual Chirality.

PubMed

Tian, Xin; Meng, Fanbin; Meng, Fanchen; Chen, Xiangnan; Guo, Yifan; Wang, Ying; Zhu, Wenjun; Zhou, Zuowan

2017-05-10

In this study, we designed a dual-chirality hierarchical structure to achieve a synergistically enhanced effect in microwave absorption via the hybridization of nanomaterials. Herein, polyaniline (PANi) nanorods with tunable chirality are grown on helical carbon nanotubes (HCNTs), a typical nanoscale chiral structure, through in situ polymerization. The experimental results show that the hierarchical hybrids (PANi@HCNTs) exhibit distinctly dual chirality and a significant enhancement in electromagnetic (EM) losses compared to those of either pure PANi or HCNTs. The maximum reflection loss of the as-prepared hybrids can reach -32.5 dB at 8.9 GHz. Further analysis demonstrates that combinations of chiral acid-doped PANi and coiled HCNTs with molecular and nanoscale chirality lead to synergistic effects resulting from the dual chirality. The so-called cross-polarization may result in additional interactions with induced EM waves in addition to multiscaled relaxations from functional groups and interfacial polarizations, which can benefit EM absorption.

Experimental evidence of a helical, supercritical instability in pipe flow of shear thinning fluids

NASA Astrophysics Data System (ADS)

Picaut, L.; Ronsin, O.; Caroli, C.; Baumberger, T.

2017-08-01

We study experimentally the flow stability of entangled polymer solutions extruded through glass capillaries. We show that the pipe flow becomes linearly unstable beyond a critical value (Wic≃5 ) of the Weissenberg number, via a supercritical bifurcation which results in a helical distortion of the extrudate. We find that the amplitude of the undulation vanishes as the aspect ratio L /R of the capillary tends to zero, and saturates for large L /R , indicating that the instability affects the whole pipe flow, rather than the contraction or exit regions. These results, when compared to previous theoretical and experimental works, lead us to argue that the nature of the instability is controlled by the level of shear thinning of the fluids. In addition, we provide strong hints that the nonlinear development of the instabiilty is mitigated, in our system, by the gradual emergence of gross wall slip.

EUV spectroscopy of highly charged high Z ions in the Large Helical Device plasmas

NASA Astrophysics Data System (ADS)

Suzuki, C.; Koike, F.; Murakami, I.; Tamura, N.; Sudo, S.; Sakaue, H. A.; Nakamura, N.; Morita, S.; Goto, M.; Kato, D.; Nakano, T.; Higashiguchi, T.; Harte, C. S.; OʼSullivan, G.

2014-11-01

We present recent results on the extreme ultraviolet (EUV) spectroscopy of highly charged high Z ions in plasmas produced in the Large Helical Device (LHD) at the National Institute for Fusion Science. Tungsten, bismuth and lanthanide elements have recently been studied in the LHD in terms of their importance in fusion research and EUV light source development. In relatively low temperature plasmas, quasicontinuum emissions from open 4d or 4f subshell ions are predominant in the EUV region, while the spectra tend to be dominated by discrete lines from open 4s or 4p subshell ions in higher temperature plasmas. Comparative analyses using theoretical calculations and charge-separated spectra observed in an electron beam ion trap have been performed to achieve better agreement with the spectra measured in the LHD. As a result, databases on Z dependence of EUV spectra in plasmas have been widely extended.

Transverse Momentum Dependence of J/psi Polarization at Midrapidity in p+p Collisions at s = 200 GeV

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

Adare, A.; Awes, Terry C; Cianciolo, Vince

We report the measurement of the transverse momentum dependence of inclusive J/{psi} polarization in p+p collisions at {radical}s = 200 GeV performed by the PHENIX Experiment at the Relativistic Heavy Ion Collider. The J/{psi} polarization is studied in the helicity, Gottfried-Jackson, and Collins-Soper frames for p{sub T} < 5 GeV/c and |y| < 0.35. The polarization in the helicity and Gottfried-Jackson frames is consistent with zero for all transverse momenta, with a slight (1.8 sigma) trend towards longitudinal polarization for transverse momenta above 2 GeV/c. No conclusion is allowed due to the limited acceptance in the Collins-Soper frame and themore » uncertainties of the current data. The results are compared to observations for other collision systems and center of mass energies and to different quarkonia production models.« less

Transverse momentum dependence of J/ψ polarization at midrapidity in p+p collisions at s=200GeV

NASA Astrophysics Data System (ADS)

Adare, A.; Afanasiev, S.; Aidala, C.; Ajitanand, N. N.; Akiba, Y.; Al-Bataineh, H.; Alexander, J.; Aoki, K.; Aphecetche, L.; Asai, J.; Atomssa, E. T.; Averbeck, R.; Awes, T. C.; Azmoun, B.; Babintsev, V.; Bai, M.; Baksay, G.; Baksay, L.; Baldisseri, A.; Barish, K. N.; Barnes, P. D.; Bassalleck, B.; Basye, A. T.; Bathe, S.; Batsouli, S.; Baublis, V.; Baumann, C.; Bazilevsky, A.; Belikov, S.; Bennett, R.; Berdnikov, A.; Berdnikov, Y.; Bickley, A. A.; Boissevain, J. G.; Borel, H.; Boyle, K.; Brooks, M. L.; Buesching, H.; Bumazhnov, V.; Bunce, G.; Butsyk, S.; Camacho, C. M.; Campbell, S.; Chang, B. S.; Chang, W. C.; Charvet, J.-L.; Chernichenko, S.; Chi, C. Y.; Chiu, M.; Choi, I. J.; Choudhury, R. K.; Chujo, T.; Chung, P.; Churyn, A.; Cianciolo, V.; Citron, Z.; Cole, B. A.; Conesa Del Valle, Z.; Constantin, P.; Csanád, M.; Csörgö, T.; Dahms, T.; Dairaku, S.; Das, K.; David, G.; Denisov, A.; D'Enterria, D.; Deshpande, A.; Desmond, E. J.; Dietzsch, O.; Dion, A.; Donadelli, M.; Drapier, O.; Drees, A.; Drees, K. A.; Dubey, A. K.; Durum, A.; Dutta, D.; Dzhordzhadze, V.; Efremenko, Y. V.; Ellinghaus, F.; Engelmore, T.; Enokizono, A.; En'Yo, H.; Esumi, S.; Eyser, K. O.; Fadem, B.; Fields, D. E.; Finger, M., Jr.; Finger, M.; Fleuret, F.; Fokin, S. L.; Fraenkel, Z.; Frantz, J. E.; Franz, A.; Frawley, A. D.; Fujiwara, K.; Fukao, Y.; Fusayasu, T.; Garishvili, I.; Glenn, A.; Gong, H.; Gonin, M.; Gosset, J.; Goto, Y.; Granier de Cassagnac, R.; Grau, N.; Greene, S. V.; Grosse Perdekamp, M.; Gunji, T.; Gustafsson, H.-Å.; Hadj Henni, A.; Haggerty, J. S.; Hamagaki, H.; Han, R.; Hartouni, E. P.; Haruna, K.; Haslum, E.; Hayano, R.; Heffner, M.; Hemmick, T. K.; Hester, T.; He, X.; Hill, J. C.; Hohlmann, M.; Holzmann, W.; Homma, K.; Hong, B.; Horaguchi, T.; Hornback, D.; Huang, S.; Ichihara, T.; Ichimiya, R.; Ikeda, Y.; Imai, K.; Imrek, J.; Inaba, M.; Isenhower, D.; Ishihara, M.; Isobe, T.; Issah, M.; Isupov, A.; Ivanischev, D.; Jacak, B. V.; Jia, J.; Jin, J.; Johnson, B. M.; Joo, K. S.; Jouan, D.; Kajihara, F.; Kametani, S.; Kamihara, N.; Kamin, J.; Kang, J. H.; Kapustinsky, J.; Kawall, D.; Kazantsev, A. V.; Kempel, T.; Khanzadeev, A.; Kijima, K. M.; Kikuchi, J.; Kim, B. I.; Kim, D. H.; Kim, D. J.; Kim, E.; Kim, S. H.; Kinney, E.; Kiriluk, K.; Kiss, A.; Kistenev, E.; Klay, J.; Klein-Boesing, C.; Kochenda, L.; Komkov, B.; Konno, M.; Koster, J.; Kozlov, A.; Král, A.; Kravitz, A.; Kunde, G. J.; Kurita, K.; Kurosawa, M.; Kweon, M. J.; Kwon, Y.; Kyle, G. S.; Lacey, R.; Lai, Y. S.; Lajoie, J. G.; Layton, D.; Lebedev, A.; Lee, D. M.; Lee, K. B.; Lee, T.; Leitch, M. J.; Leite, M. A. L.; Lenzi, B.; Liebing, P.; Liška, T.; Litvinenko, A.; Liu, H.; Liu, M. X.; Li, X.; Love, B.; Lynch, D.; Maguire, C. F.; Makdisi, Y. I.; Malakhov, A.; Malik, M. D.; Manko, V. I.; Mannel, E.; Mao, Y.; Mašek, L.; Masui, H.; Matathias, F.; McCumber, M.; McGaughey, P. L.; Means, N.; Meredith, B.; Miake, Y.; Mikeš, P.; Miki, K.; Milov, A.; Mishra, M.; Mitchell, J. T.; Mohanty, A. K.; Morino, Y.; Morreale, A.; Morrison, D. P.; Moukhanova, T. V.; Mukhopadhyay, D.; Murata, J.; Nagamiya, S.; Nagle, J. L.; Naglis, M.; Nagy, M. I.; Nakagawa, I.; Nakamiya, Y.; Nakamura, T.; Nakano, K.; Newby, J.; Nguyen, M.; Niita, T.; Nouicer, R.; Nyanin, A. S.; O'Brien, E.; Oda, S. X.; Ogilvie, C. A.; Okada, H.; Okada, K.; Oka, M.; Onuki, Y.; Oskarsson, A.; Ouchida, M.; Ozawa, K.; Pak, R.; Palounek, A. P. T.; Pantuev, V.; Papavassiliou, V.; Park, J.; Park, W. J.; Pate, S. F.; Pei, H.; Peng, J.-C.; Pereira, H.; Peresedov, V.; Peressounko, D. Yu.; Pinkenburg, C.; Purschke, M. L.; Purwar, A. K.; Qu, H.; Rak, J.; Rakotozafindrabe, A.; Ravinovich, I.; Read, K. F.; Rembeczki, S.; Reygers, K.; Riabov, V.; Riabov, Y.; Roach, D.; Roche, G.; Rolnick, S. D.; Rosati, M.; Rosendahl, S. S. E.; Rosnet, P.; Rukoyatkin, P.; Ružička, P.; Rykov, V. L.; Sahlmueller, B.; Saito, N.; Sakaguchi, T.; Sakai, S.; Sakashita, K.; Samsonov, V.; Sato, T.; Sawada, S.; Sedgwick, K.; Seele, J.; Seidl, R.; Semenov, A. Yu.; Semenov, V.; Seto, R.; Sharma, D.; Shein, I.; Shibata, T.-A.; Shigaki, K.; 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.; Soldatov, A.; Soltz, R. A.; Sondheim, W. E.; Sorensen, S. P.; Sourikova, I. V.; Staley, F.; Stankus, P. W.; Stenlund, E.; Stepanov, M.; Ster, A.; Stoll, S. P.; Sugitate, T.; Suire, C.; Sukhanov, A.; Sziklai, J.; Takagui, E. M.; Taketani, A.; Tanabe, R.; Tanaka, Y.; Tanida, K.; Tannenbaum, M. J.; Taranenko, A.; Tarján, P.; Themann, H.; Thomas, T. L.; Togawa, M.; Toia, A.; Tomášek, L.; Tomita, Y.; Torii, H.; Towell, R. S.; Tram, V.-N.; Tserruya, I.; Tsuchimoto, Y.; Vale, C.; Valle, H.; van Hecke, H. W.; Veicht, A.; Velkovska, J.; Vertesi, R.; Vinogradov, A. A.; Virius, M.; Vrba, V.; Vznuzdaev, E.; Wang, X. R.; Watanabe, Y.; Wei, F.; Wessels, J.; White, S. N.; Winter, D.; Woody, C. L.; Wysocki, M.; Xie, W.; Yamaguchi, Y. L.; Yamaura, K.; Yang, R.; Yanovich, A.; Ying, J.; Yokkaichi, S.; Young, G. R.; Younus, I.; Yushmanov, I. E.; Zajc, W. A.; Zaudtke, O.; Zhang, C.; Zhou, S.; Zolin, L.; PHENIX Collaboration

2010-07-01

We report the measurement of the transverse momentum dependence of inclusive J/ψ polarization in p+p collisions at s=200GeV performed by the PHENIX Experiment at the Relativistic Heavy Ion Collider. The J/ψ polarization is studied in the helicity, Gottfried-Jackson, and Collins-Soper frames for pT<5GeV/c and |y|<0.35. The polarization in the helicity and Gottfried-Jackson frames is consistent with zero for all transverse momenta, with a slight (1.8 sigma) trend towards longitudinal polarization for transverse momenta above 2GeV/c. No conclusion is allowed due to the limited acceptance in the Collins-Soper frame and the uncertainties of the current data. The results are compared to observations for other collision systems and center of mass energies and to different quarkonia production models.

Transverse momentum dependence of J/{psi} polarization at midrapidity in p+p collisions at {radical}(s)=200 GeV

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

Adare, A.; Bickley, A. A.; Ellinghaus, F.

We report the measurement of the transverse momentum dependence of inclusive J/{psi} polarization in p+p collisions at {radical}(s)=200 GeV performed by the PHENIX Experiment at the Relativistic Heavy Ion Collider. The J/{psi} polarization is studied in the helicity, Gottfried-Jackson, and Collins-Soper frames for p{sub T}<5 GeV/c and |y|<0.35. The polarization in the helicity and Gottfried-Jackson frames is consistent with zero for all transverse momenta, with a slight (1.8 sigma) trend towards longitudinal polarization for transverse momenta above 2 GeV/c. No conclusion is allowed due to the limited acceptance in the Collins-Soper frame and the uncertainties of the current data. Themore » results are compared to observations for other collision systems and center of mass energies and to different quarkonia production models.« less

Effect of the helicity injection rate and the Lundquist number on spheromak sustainment

NASA Astrophysics Data System (ADS)

García-Martínez, Pablo Luis; Lampugnani, Leandro Gabriel; Farengo, Ricardo

2014-12-01

The dynamics of the magnetic relaxation process during the sustainment of spheromak configurations at different helicity injection rates is studied. The three-dimensional activity is recovered using time-dependent resistive magnetohydrodynamic simulations. A cylindrical flux conserver with concentric electrodes is used to model configurations driven by a magnetized coaxial gun. Magnetic helicity is injected by tangential boundary flows. Different regimes of sustainment are identified and characterized in terms of the safety factor profile. The spatial and temporal behavior of fluctuations is described. The dynamo action is shown to be in close agreement with existing experimental data. These results are relevant to the design and operation of helicity injected devices, as well as to basic understanding of the plasma relaxation mechanism in quasi-steady state.

Helicity moduli of three-dimensional dilute XY models

NASA Astrophysics Data System (ADS)

Garg, Anupam; Pandit, Rahul; Solla, Sara A.; Ebner, C.

1984-07-01

The helicity moduli of various dilute, classical XY models on three-dimensional lattices are studied with a view to understanding some aspects of the superfluidity of 4He in Vycor glass. A spinwave calculation is used to obtain the low-temperature helicity modulus of a regularly-diluted XY model. A similar calculation is performed for the randomly bond-diluted and site-diluted XY models in the limit of low dilution. A Monte Carlo simulation is used to obtain the helicity modulus of the randomly bond-diluted XY model over a wide range of temperature and dilution. It is found that the randomly diluted models do agree and the regularly diluted model does not agree with certain experimentally found features of the variation in superfluid fraction with coverage of 4He in Vycor glass.

PROMINENCE FORMATION ASSOCIATED WITH AN EMERGING HELICAL FLUX ROPE

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

Okamoto, Takenori J.; Tsuneta, Saku; Katsukawa, Yukio

2009-05-20

The formation and evolution process and magnetic configuration of solar prominences remain unclear. In order to study the formation process of prominences, we examine continuous observations of a prominence in NOAA AR 10953 with the Solar Optical Telescope on the Hinode satellite. As reported in our previous Letter, we find a signature suggesting that a helical flux rope emerges from below the photosphere under a pre-existing prominence. Here we investigate more detailed properties and photospheric indications of the emerging helical flux rope, and discuss their relationship to the formation of the prominence. Our main conclusions are: (1) a dark regionmore » with absence of strong vertical magnetic fields broadens and then narrows in Ca II H-line filtergrams. This phenomenon is consistent with the emergence of the helical flux rope as photospheric counterparts. The size of the flux rope is roughly 30,000 km long and 10,000 km wide. The width is larger than that of the prominence. (2) No shear motion or converging flows are detected, but we find diverging flows such as mesogranules along the polarity inversion line. The presence of mesogranules may be related to the emergence of the helical flux rope. (3) The emerging helical flux rope reconnects with magnetic fields of the pre-existing prominence to stabilize the prominence for the next several days. We thus conjecture that prominence coronal magnetic fields emerge in the form of helical flux ropes that contribute to the formation and maintenance of the prominence.« less

Benchmark of the local drift-kinetic models for neoclassical transport simulation in helical plasmas

NASA Astrophysics Data System (ADS)

Huang, B.; Satake, S.; Kanno, R.; Sugama, H.; Matsuoka, S.

2017-02-01

The benchmarks of the neoclassical transport codes based on the several local drift-kinetic models are reported here. Here, the drift-kinetic models are zero orbit width (ZOW), zero magnetic drift, DKES-like, and global, as classified in Matsuoka et al. [Phys. Plasmas 22, 072511 (2015)]. The magnetic geometries of Helically Symmetric Experiment, Large Helical Device (LHD), and Wendelstein 7-X are employed in the benchmarks. It is found that the assumption of E ×B incompressibility causes discrepancy of neoclassical radial flux and parallel flow among the models when E ×B is sufficiently large compared to the magnetic drift velocities. For example, Mp≤0.4 where Mp is the poloidal Mach number. On the other hand, when E ×B and the magnetic drift velocities are comparable, the tangential magnetic drift, which is included in both the global and ZOW models, fills the role of suppressing unphysical peaking of neoclassical radial-fluxes found in the other local models at Er≃0 . In low collisionality plasmas, in particular, the tangential drift effect works well to suppress such unphysical behavior of the radial transport caused in the simulations. It is demonstrated that the ZOW model has the advantage of mitigating the unphysical behavior in the several magnetic geometries, and that it also implements the evaluation of bootstrap current in LHD with the low computation cost compared to the global model.

Helicity in the dynamic magnetotail

NASA Astrophysics Data System (ADS)

Buchert, Stephan

Observations of substorms typically feature a clear azimuthal or east-west asymmetry which has been described in expressions like for example westward-traveling surge. The origin of this asymmetry is not clear. Candidates are the Hall effect, either in the ionosphere, or in magnetic reconnection, and self-induction when Hall currents change in time. The magnetic helicity in the tail measured by the Cluster satellites shows a clear preference during dynamic events, that we have studied. We discuss possible causes of this non-zero helicity and whether it is related to east-west assymmetric tail dynamics.

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.

The global distribution of magnetic helicity in the solar corona

NASA Astrophysics Data System (ADS)

Yeates, A. R.; Hornig, G.

2016-10-01

By defining an appropriate field line helicity, we apply the powerful concept of magnetic helicity to the problem of global magnetic field evolution in the Sun's corona. As an ideal-magnetohydrodynamic invariant, the field line helicity is a meaningful measure of how magnetic helicity is distributed within the coronal volume. It may be interpreted, for each magnetic field line, as a magnetic flux linking with that field line. Using magneto-frictional simulations, we investigate how field line helicity evolves in the non-potential corona as a result of shearing by large-scale motions on the solar surface. On open magnetic field lines, the helicity injected by the Sun is largely output to the solar wind, provided that the coronal relaxation is sufficiently fast. But on closed magnetic field lines, helicity is able to build up. We find that the field line helicity is non-uniformly distributed, and is highly concentrated in twisted magnetic flux ropes. Eruption of these flux ropes is shown to lead to sudden bursts of helicity output, in contrast to the steady flux along the open magnetic field lines. Movies are available at http://www.aanda.org

Comparison of magnetic helicity close to the sun and in magnetic clouds

NASA Astrophysics Data System (ADS)

Rust, D.

Magnetic helicity is present in the solar atmosphere - as inferred from vector magnetograph measurements, solar filaments, S-shaped coronal structures known as sigmoids, and sunspot whorls. I will survey the possible solar sources of this magnetic helicity. Included are fieldline footpoint motions, effects of Coriolis forces, effects of convection, shear associated with differential rotation, and, of course, the internal dynamo. Besides the survey of possible local mechanisms for helicity generation, I will consider the global view of the flow of helicity from the sun into interplanetary space. The principal agents by which the sun sheds helicity are coronal mass ejections (CMEs). They are often associated with interplanetary magnetic clouds (MCs), whose fields are regularly probed with sensitive spacecraft magnetometers. MCs yield more direct measurements of helicity. They show that each MC carries helicity away from the sun. A major issue in solar-heliospheric research is whether the amount of helicity that MCs carry away in a solar cycle can be accounted for by the helicity generation mechanisms proposed so far. The NASA Solar and Heliospheric Physics Program supports this work under grants NAG5- 7921 and NAG 5-11584.

Probing topology and dynamics of the second transmembrane domain (M2δ) of the acetyl choline receptor using magnetically aligned lipid bilayers (bicelles) and EPR spectroscopy.

PubMed

Sahu, Indra D; Mayo, Daniel J; Subbaraman, Nidhi; Inbaraj, Johnson J; McCarrick, Robert M; Lorigan, Gary A

2017-08-01

Characterizing membrane protein structure and dynamics in the lipid bilayer membrane is very important but experimentally challenging. EPR spectroscopy offers a unique set of techniques to investigate a membrane protein structure, dynamics, topology, and distance constraints in lipid bilayers. Previously our lab demonstrated the use of magnetically aligned phospholipid bilayers (bicelles) for probing topology and dynamics of the membrane peptide M2δ of the acetyl choline receptor (AchR) as a proof of concept. In this study, magnetically aligned phospholipid bilayers and rigid spin labels were further utilized to provide improved dynamic information and topology of M2δ peptide. Seven TOAC-labeled AchR M2δ peptides were synthesized to demonstrate the utility of a multi-labeling amino acid substitution alignment strategy. Our data revealed the helical tilts to be 11°, 17°, 9°, 17°, 16°, 11°, 9°±4° for residues I7TOAC, Q13TOAC, A14TOAC, V15TOAC, C16TOAC, L17TOAC, and L18TOAC, respectively. The average helical tilt of the M2δ peptide was determined to be ∼13°. This study also revealed that the TOAC labels were attached to the M2δ peptide with different dynamics suggesting that the sites towards the C-terminal end are more rigid when compared to the sites towards the N-terminus. The dynamics of the TOAC labeled sites were more resolved in the aligned samples when compared to the randomly disordered samples. This study highlights the use of magnetically aligned lipid bilayer EPR technique to determine a more accurate helical tilt and more resolved local dynamics of AchR M2δ peptide. Copyright © 2017 Elsevier B.V. All rights reserved.

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

Reigel, M. M.; Fowley, M. D.; Pickenheim, B. R.

A soft metal with low wear resistance (6000 series aluminum), was used to minimize run time while maximizing wear rate. Two paddle configurations were tested, with the first four paddles after the augers replaced by the wear paddles. The first configuration was all flat paddles, with the first paddle not aligned with the augers and is consistent with present SPF mixer. The second configuration had helical paddles for the first three stages after the augers and a flat paddle at the fourth stage. The first helical paddle was aligned with the auger flight for the second configuration. The all flatmore » paddle configuration wear rate was approximately double the wear rate of the helical paddles for the first two sets of paddles after the augers. For both configurations, there was little or no wear on the third and fourth paddle sets based on mass change, indicating that the fully wetted premix materials are much less abrasive than the un-wetted or partially wetted premix. Additionally, inspection of the wear surface of the paddles at higher magnification showed the flat paddles were worn much more than the helical and is consistent with the wear rates. Aligning the auger discharge flight with the first set of helical paddles was effective in reducing the wear rate as compared to the flat paddle configuration. Changing the paddle configuration from flat to helical resulted in a slight increase in rheological properties. Although, both tests produced grout-like material that is within the processing rage of the SPF, it should be noted that cement is not included in the premix and water was used rather than salt solution, which does affect the rheology of the fresh grout. The higher rheological properties from the helical wear test are most likely due to the reduced number of shearing paddles in the mixer. In addition, there is variation in the rheological data for each wear test. This is most likely due to the way that the dry feeds enter the mixer from the dry feeder. The premix is discharged from the hopper in an unsteady fashion, where irregular sized clumps were observed leaving the discharge of the auger, though the auger speed is constant.« less

A rigid motion correction method for helical computed tomography (CT)

NASA Astrophysics Data System (ADS)

Kim, J.-H.; Nuyts, J.; Kyme, A.; Kuncic, Z.; Fulton, R.

2015-03-01

We propose a method to compensate for six degree-of-freedom rigid motion in helical CT of the head. The method is demonstrated in simulations and in helical scans performed on a 16-slice CT scanner. Scans of a Hoffman brain phantom were acquired while an optical motion tracking system recorded the motion of the bed and the phantom. Motion correction was performed by restoring projection consistency using data from the motion tracking system, and reconstructing with an iterative fully 3D algorithm. Motion correction accuracy was evaluated by comparing reconstructed images with a stationary reference scan. We also investigated the effects on accuracy of tracker sampling rate, measurement jitter, interpolation of tracker measurements, and the synchronization of motion data and CT projections. After optimization of these aspects, motion corrected images corresponded remarkably closely to images of the stationary phantom with correlation and similarity coefficients both above 0.9. We performed a simulation study using volunteer head motion and found similarly that our method is capable of compensating effectively for realistic human head movements. To the best of our knowledge, this is the first practical demonstration of generalized rigid motion correction in helical CT. Its clinical value, which we have yet to explore, may be significant. For example it could reduce the necessity for repeat scans and resource-intensive anesthetic and sedation procedures in patient groups prone to motion, such as young children. It is not only applicable to dedicated CT imaging, but also to hybrid PET/CT and SPECT/CT, where it could also ensure an accurate CT image for lesion localization and attenuation correction of the functional image data.

Identifying intrinsically disordered protein regions likely to undergo binding-induced helical transitions.

PubMed

Glover, Karen; Mei, Yang; Sinha, Sangita C

2016-10-01

Many proteins contain intrinsically disordered regions (IDRs) lacking stable secondary and ordered tertiary structure. IDRs are often implicated in macromolecular interactions, and may undergo structural transitions upon binding to interaction partners. However, as binding partners of many protein IDRs are unknown, these structural transitions are difficult to verify and often are poorly understood. In this study we describe a method to identify IDRs that are likely to undergo helical transitions upon binding. This method combines bioinformatics analyses followed by circular dichroism spectroscopy to monitor 2,2,2-trifluoroethanol (TFE)-induced changes in secondary structure content of these IDRs. Our results demonstrate that there is no significant change in the helicity of IDRs that are not predicted to fold upon binding. IDRs that are predicted to fold fall into two groups: one group does not become helical in the presence of TFE and includes examples of IDRs that form β-strands upon binding, while the other group becomes more helical and includes examples that are known to fold into helices upon binding. Therefore, we propose that bioinformatics analyses combined with experimental evaluation using TFE may provide a general method to identify IDRs that undergo binding-induced disorder-to-helix transitions. Copyright © 2016 Elsevier B.V. All rights reserved.

Computer Modeling of Protocellular Functions: Peptide Insertion in Membranes

NASA Technical Reports Server (NTRS)

Rodriquez-Gomez, D.; Darve, E.; Pohorille, A.

2006-01-01

Lipid vesicles became the precursors to protocells by acquiring the capabilities needed to survive and reproduce. These include transport of ions, nutrients and waste products across cell walls and capture of energy and its conversion into a chemically usable form. In modem organisms these functions are carried out by membrane-bound proteins (about 30% of the genome codes for this kind of proteins). A number of properties of alpha-helical peptides suggest that their associations are excellent candidates for protobiological precursors of proteins. In particular, some simple a-helical peptides can aggregate spontaneously and form functional channels. This process can be described conceptually by a three-step thermodynamic cycle: 1 - folding of helices at the water-membrane interface, 2 - helix insertion into the lipid bilayer and 3 - specific interactions of these helices that result in functional tertiary structures. Although a crucial step, helix insertion has not been adequately studied because of the insolubility and aggregation of hydrophobic peptides. In this work, we use computer simulation methods (Molecular Dynamics) to characterize the energetics of helix insertion and we discuss its importance in an evolutionary context. Specifically, helices could self-assemble only if their interactions were sufficiently strong to compensate the unfavorable Free Energy of insertion of individual helices into membranes, providing a selection mechanism for protobiological evolution.

ANATOMY OF HELICAL EXTRAGALACTIC JETS: THE CASE OF S5 0836+710

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

Perucho, M.; Kovalev, Y. Y.; Lobanov, A. P.

Helical structures are common in extragalactic jets. They are usually attributed in the literature to periodical phenomena in the source (e.g., precession). In this work, we use very long baseline interferometry data of the radio jet in the quasar S5 0836+710 and hypothesize that the ridgeline of helical jets like this corresponds to a pressure maximum in the jet and assume that the helically twisted pressure maximum is the result of a helical wave pattern. For our study, we use observations of the jet in S5 0836+710 at different frequencies and epochs. The results show that the structures observed aremore » physical and not generated artificially by the observing arrays. Our hypothesis that the observed intensity ridgeline can correspond to a helically twisted pressure maximum is confirmed by our observational tests. This interpretation allows us to explain jet misalignment between parsec and kiloparsec scales when the viewing angle is small, and also brings us to the conclusion that high-frequency observations may show only a small region of the jet flow concentrated around the maximum pressure ridgeline observed at low frequencies. Our work provides a potential explanation for the apparent transversal superluminal speeds observed in several extragalactic jets by means of transversal shift of an apparent core position with time.« less

Morphology of blazar-induced gamma ray halos due to a helical intergalactic magnetic field

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

Long, Andrew J.; Vachaspati, Tanmay, E-mail: andrewjlong@asu.edu, E-mail: tvachasp@asu.edu

We study the characteristic size and shape of idealized blazar-induced cascade halos in the 1–100,GeV energy range assuming various non-helical and helical configurations for the intergalactic magnetic field (IGMF). While the magnetic field creates an extended halo, the helicity provides the halo with a twist. Under simplifying assumptions, we assess the parameter regimes for which it is possible to measure the size and shape of the halo from a single source and then to deduce properties of the IGMF. We find that blazar halo measurements with an experiment similar to Fermi-LAT are best suited to probe a helical magnetic fieldmore » with strength and coherence length today in the ranges 10{sup −17} ∼< B{sub 0} / Gauss ∼< 10{sup −13} and 10 Mpc ∼< λ ∼< 10 Gpc where H ∼ B{sub 0}{sup 2} / λ is the magnetic helicity density. Stronger magnetic fields or smaller coherence scales can still potentially be investigated, but the connection between the halo morphology and the magnetic field properties is more involved. Weaker magnetic fields or longer coherence scales require high photon statistics or superior angular resolution.« less

Homooligomeric β3 (R)-valine peptides: Transformation between C14 and C12 helical structures induced by a guest Aib residue.

PubMed

Vasantha, Basavalingappa; George, Gijo; Raghothama, Srinivasarao; Balaram, Padmanabhan

2017-01-01

Novel helical, structures unprecedented in the chemistry of α-polypeptides, may be found in polypeptides containing β and γ amino acids. The structural characterization of C 12 and C 14 -helices in oligo β-peptides was originally achieved using conformationally constrained cyclic β-residues. This study explores the conformational characteristics of proteinogenic β 3 residues in homooligomeric sequences and addresses the issue of inducing a transition between C 14 and C 12 helices by the introduction of a guest α-residue. Folded C 14 -helical structures are demonstrated for the nonapeptide Boc-[β 3 (R)Val] 9 -OMe by NMR methods in CDCl 3 -DMSO mixtures, while the peptide was found to be aggregated in CDCl 3 . The insertion of a guest Aib residue into an oligo-β-valine sequence in the octapeptide model Boc-[(β 3 (R)Val) 3 -Aib-(β 3 (R)Val] 4 -OMe results in well dispersed NH region in the NMR spectrum indicating folded structures in CDCl 3 . Structure calculations for both the peptides using NOE distance constraints support a C 14 helical structure in the homooligomer which transform into a C 12 helix on introduction of the guest Aib residue. © 2016 Wiley Periodicals, Inc.

Helical Antimicrobial Sulfono- {gamma} -AApeptides

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

Li, Yaqiong; Wu, Haifan; Teng, Peng

Host-defense peptides (HDPs) such as magainin 2 have emerged as potential therapeutic agents combating antibiotic resistance. Inspired by their structures and mechanism of action, herein we report the fi rst example of antimicrobial helical sulfono- γ - AApeptide foldamers. The lead molecule displays broad-spectrum and potent antimicrobial activity against multi-drug-resistant Gram- positive and Gram-negative bacterial pathogens. Time-kill studies and fl uorescence microscopy suggest that sulfono- γ -AApeptides eradicate bacteria by taking a mode of action analogous to that of HDPs. Clear structure - function relationships exist in the studied sequences. Longer sequences, presumably adopting more-de fi ned helical structures, aremore » more potent than shorter ones. Interestingly, the sequence with less helical propensity in solution could be more selective than the stronger helix-forming sequences. Moreover, this class of antimicrobial agents are resistant to proteolytic degradation. These results may lead to the development of a new class of antimicrobial foldamers combating emerging antibiotic-resistant pathogens.« less

Emergent perversions in the buckling of heterogeneous elastic strips

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

Liu, Shuangping; Yao, Zhenwei; Chiou, Kevin

A perversion in an otherwise uniform helical structure, such as a climbing plant tendril, refers to a kink that connects two helices with opposite chiralities. Such singularity structures are widely seen in natural and artificial mechanical systems, and they provide the fundamental mechanism of helical symmetry breaking. However, it is still not clear how perversions arise in various helical structures and which universal principles govern them. As such, a heterogeneous elastic bistrip system provides an excellent model to address these questions. In this paper, we investigate intrinsic perversion properties which are independent of strip shapes. This study reveals the richmore » physics of perversions in the 3D elastic system, including the condensation of strain energy over perversions during their formation, the repulsive nature of the perversion–perversion interaction, and the coalescence of perversions that finally leads to a linear defect structure. Finally, this study may have implications for understanding relevant biological motifs and for use of perversions as energy storers in the design of micromuscles and soft robotics.« less

Hydrogen bonds and heat diffusion in α-helices: a computational study.

PubMed

Miño, German; Barriga, Raul; Gutierrez, Gonzalo

2014-08-28

Recent evidence has shown a correlation between the heat diffusion pathways and the known allosteric communication pathways in proteins. Allosteric communication in proteins is a central, yet unsolved, problem in biochemistry, and the study and characterization of the structural determinants that mediate energy transfer among different parts of proteins is of major importance. In this work, we characterized the role of hydrogen bonds in diffusivity of thermal energy for two sets of α-helices with different abilities to form hydrogen bonds. These hydrogen bonds can be a constitutive part of the α-helices or can arise from the lateral chains. In our in vacuo simulations, it was observed that α-helices with a higher possibility of forming hydrogen bonds also had higher rates of thermalization. Our simulations also revealed that heat readily flowed through atoms involved in hydrogen bonds. As a general conclusion, according to our simulations, hydrogen bonds fulfilled an important role in heat diffusion in structural patters of proteins.

Emergent perversions in the buckling of heterogeneous elastic strips

DOE PAGES

Liu, Shuangping; Yao, Zhenwei; Chiou, Kevin; ...

2016-06-14

A perversion in an otherwise uniform helical structure, such as a climbing plant tendril, refers to a kink that connects two helices with opposite chiralities. Such singularity structures are widely seen in natural and artificial mechanical systems, and they provide the fundamental mechanism of helical symmetry breaking. However, it is still not clear how perversions arise in various helical structures and which universal principles govern them. As such, a heterogeneous elastic bistrip system provides an excellent model to address these questions. In this paper, we investigate intrinsic perversion properties which are independent of strip shapes. This study reveals the richmore » physics of perversions in the 3D elastic system, including the condensation of strain energy over perversions during their formation, the repulsive nature of the perversion–perversion interaction, and the coalescence of perversions that finally leads to a linear defect structure. Finally, this study may have implications for understanding relevant biological motifs and for use of perversions as energy storers in the design of micromuscles and soft robotics.« less

Molecular modelling indicates that the pathological conformations of prion proteins might be beta-helical.

PubMed Central

Downing, D T; Lazo, N D

1999-01-01

Creutzfeldt-Jakob disease, kuru, scrapie and bovine spongiform encephalopathy are diseases of the mammalian central nervous system that involve the conversion of a cellular protein into an insoluble extracellular isoform. Spectroscopic studies have shown that the precursor protein contains mainly alpha-helical and random-coil conformations, whereas the prion isoform is largely in the beta conformation. The pathogenic prion is resistant to denaturation and protease digestion and can promote the conversion of the precursor protein to the pathogenic form. These properties have yet to be explained in terms of the structural conformations of the proteins. In the present study, molecular modelling showed that prion proteins could adopt the beta-helical conformation, which has been established for a number of fibrous proteins and has been suggested previously as the basis of amyloid fibrils. The beta-helical conformation provides explanations for the biophysical and biochemical stability of prions, their ability to form templates for the transmission of pathological conformation, and the existence of phenotypical strains of the prion diseases. PMID:10510313

Mean-field dynamo in a turbulence with shear and kinetic helicity fluctuations.

PubMed

Kleeorin, Nathan; Rogachevskii, Igor

2008-03-01

We study the effects of kinetic helicity fluctuations in a turbulence with large-scale shear using two different approaches: the spectral tau approximation and the second-order correlation approximation (or first-order smoothing approximation). These two approaches demonstrate that homogeneous kinetic helicity fluctuations alone with zero mean value in a sheared homogeneous turbulence cannot cause a large-scale dynamo. A mean-field dynamo is possible when the kinetic helicity fluctuations are inhomogeneous, which causes a nonzero mean alpha effect in a sheared turbulence. On the other hand, the shear-current effect can generate a large-scale magnetic field even in a homogeneous nonhelical turbulence with large-scale shear. This effect was investigated previously for large hydrodynamic and magnetic Reynolds numbers. In this study we examine the threshold required for the shear-current dynamo versus Reynolds number. We demonstrate that there is no need for a developed inertial range in order to maintain the shear-current dynamo (e.g., the threshold in the Reynolds number is of the order of 1).

Autonomously folded α-helical lockers promote RNAi*

NASA Astrophysics Data System (ADS)

Guyader, Christian P. E.; Lamarre, Baptiste; de Santis, Emiliana; Noble, James E.; Slater, Nigel K.; Ryadnov, Maxim G.

2016-10-01

RNAi is an indispensable research tool with a substantial therapeutic potential. However, the complete transition of the approach to an applied capability remains hampered due to poorly understood relationships between siRNA delivery and gene suppression. Here we propose that interfacial tertiary contacts between α-helices can regulate siRNA cytoplasmic delivery and RNAi. We introduce a rationale of helical amphipathic lockers that differentiates autonomously folded helices, which promote gene silencing, from helices folded with siRNA, which do not. Each of the helical designs can deliver siRNA into cells via energy-dependent endocytosis, while only autonomously folded helices with pre-locked hydrophobic interfaces were able to promote statistically appreciable gene silencing. We propose that it is the amphipathic locking of interfacing helices prior to binding to siRNA that enables RNAi. The rationale offers structurally balanced amphipathic scaffolds to advance the exploitation of functional RNAi.

Autonomously folded α-helical lockers promote RNAi*

PubMed Central

Guyader, Christian P. E.; Lamarre, Baptiste; De Santis, Emiliana; Noble, James E.; Slater, Nigel K.; Ryadnov, Maxim G.

2016-01-01

RNAi is an indispensable research tool with a substantial therapeutic potential. However, the complete transition of the approach to an applied capability remains hampered due to poorly understood relationships between siRNA delivery and gene suppression. Here we propose that interfacial tertiary contacts between α-helices can regulate siRNA cytoplasmic delivery and RNAi. We introduce a rationale of helical amphipathic lockers that differentiates autonomously folded helices, which promote gene silencing, from helices folded with siRNA, which do not. Each of the helical designs can deliver siRNA into cells via energy-dependent endocytosis, while only autonomously folded helices with pre-locked hydrophobic interfaces were able to promote statistically appreciable gene silencing. We propose that it is the amphipathic locking of interfacing helices prior to binding to siRNA that enables RNAi. The rationale offers structurally balanced amphipathic scaffolds to advance the exploitation of functional RNAi. PMID:27721465

Autonomously folded α-helical lockers promote RNAi.

PubMed

Guyader, Christian P E; Lamarre, Baptiste; De Santis, Emiliana; Noble, James E; Slater, Nigel K; Ryadnov, Maxim G

2016-10-10

RNAi is an indispensable research tool with a substantial therapeutic potential. However, the complete transition of the approach to an applied capability remains hampered due to poorly understood relationships between siRNA delivery and gene suppression. Here we propose that interfacial tertiary contacts between α-helices can regulate siRNA cytoplasmic delivery and RNAi. We introduce a rationale of helical amphipathic lockers that differentiates autonomously folded helices, which promote gene silencing, from helices folded with siRNA, which do not. Each of the helical designs can deliver siRNA into cells via energy-dependent endocytosis, while only autonomously folded helices with pre-locked hydrophobic interfaces were able to promote statistically appreciable gene silencing. We propose that it is the amphipathic locking of interfacing helices prior to binding to siRNA that enables RNAi. The rationale offers structurally balanced amphipathic scaffolds to advance the exploitation of functional RNAi.

Self-Assembly of Helical Ribbons

NASA Astrophysics Data System (ADS)

Zastavker, Yevgeniya V.; Asherie, Neer; Lomakin, Aleksey; Pande, Jayanti; Donovan, Joanne M.; Schnur, Joel M.; Benedek, George B.

1999-07-01

The self-assembly of helical ribbons is examined in a variety of multicomponent enantiomerically pure systems that contain a bile salt or a nonionic detergent, a phosphatidylcholine or a fatty acid, and a steroid analog of cholesterol. In almost all systems, two different pitch types of helical ribbons are observed: high pitch, with a pitch angle of 54± 2 degrees, and low pitch, with a pitch angle of 11± 2 degrees. Although the majority of these helices are right-handed, a small proportion of left-handed helices is observed. Additionally, a third type of helical ribbon, with a pitch angle in the range 30-47 degrees, is occasionally found. These experimental findings suggest that the helical ribbons are crystalline rather than liquid crystal in nature and also suggest that molecular chirality may not be the determining factor in helix formation. The large yields of helices produced will permit a systematic investigation of their individual kinetic evolution and their elastic moduli.

Solution conformation of a peptide fragment representing a proposed RNA-binding site of a viral coat protein studied by two-dimensional NMR

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

van der Graaf, M.; van Mierlo, C.P.M.; Hemminga, M.A.

1991-06-11

The first 25 amino acids of the coat protein of cowpea chlorotic mottle virus are essential for binding the encapsidated RNA. Although an {alpha}-helical conformation has been predicted for this highly positively charged N-terminal region. No experimental evidence for this conformation has been presented so far. In this study, two-dimensional proton NMR experiments were performed on a chemically synthesized pentacosapeptide containing the first 25 amino acids of this coat protein. All resonances could be assigned by a combined use of two-dimensional correlated spectroscopy and nuclear Overhauser enhancement spectroscopy carried out at four different temperatures. Various NMR parameters indicate the presencemore » of a conformational ensemble consisting of helical structures rapidly converting into more extended states. Differences in chemical shifts and nuclear Overhauser effects indicate that lowering the temperature induces a shift of the dynamic equilibrium toward more helical structures. At 10{degrees}C, a perceptible fraction of the conformational ensemble consists of structures with an {alpha}-helical conformation between residues 9 and 17, likely starting with a turnlike structure around Thr9 and Arg10. Both the conformation and the position of this helical region agree well with the secondary structure predictions mentioned above.« less

Computer-aided diagnosis workstation and database system for chest diagnosis based on multi-helical CT images

NASA Astrophysics Data System (ADS)

Satoh, Hitoshi; Niki, Noboru; Mori, Kiyoshi; Eguchi, Kenji; Kaneko, Masahiro; Kakinuma, Ryutarou; Moriyama, Noriyuki; Ohmatsu, Hironobu; Masuda, Hideo; Machida, Suguru; Sasagawa, Michizou

2006-03-01

Multi-helical CT scanner advanced remarkably at the speed at which the chest CT images were acquired for mass screening. Mass screening based on multi-helical CT images requires a considerable number of images to be read. It is this time-consuming step that makes the use of helical CT for mass screening impractical at present. To overcome this problem, we have provided diagnostic assistance methods to medical screening specialists by developing a lung cancer screening algorithm that automatically detects suspected lung cancers in helical CT images and a coronary artery calcification screening algorithm that automatically detects suspected coronary artery calcification. We also have developed electronic medical recording system and prototype internet system for the community health in two or more regions by using the Virtual Private Network router and Biometric fingerprint authentication system and Biometric face authentication system for safety of medical information. Based on these diagnostic assistance methods, we have now developed a new computer-aided workstation and database that can display suspected lesions three-dimensionally in a short time. This paper describes basic studies that have been conducted to evaluate this new system. The results of this study indicate that our computer-aided diagnosis workstation and network system can increase diagnostic speed, diagnostic accuracy and safety of medical information.

Several Human Liver Cell Expressed Apolipoproteins Complement HCV Virus Production with Varying Efficacy Conferring Differential Specific Infectivity to Released Viruses.

PubMed

Hueging, Kathrin; Weller, Romy; Doepke, Mandy; Vieyres, Gabrielle; Todt, Daniel; Wölk, Benno; Vondran, Florian W R; Geffers, Robert; Lauber, Chris; Kaderali, Lars; Penin, François; Pietschmann, Thomas

2015-01-01

Apolipoprotein E (ApoE), an exchangeable apolipoprotein, is necessary for production of infectious Hepatitis C virus (HCV) particles. However, ApoE is not the only liver-expressed apolipoprotein and the role of other apolipoproteins for production of infectious HCV progeny is incompletely defined. Therefore, we quantified mRNA expression of human apolipoproteins in primary human hepatocytes. Subsequently, cDNAs encoding apolipoproteins were expressed in 293T/miR-122 cells to explore if they complement HCV virus production in cells that are non-permissive due to limiting endogenous levels of human apolipoproteins. Primary human hepatocytes expressed high mRNA levels of ApoA1, A2, C1, C3, E, and H. ApoA4, A5, B, D, F, J, L1, L2, L3, L4, L6, M, and O were expressed at intermediate levels, and C2, C4, and L5 were not detected. All members of the ApoA and ApoC family of lipoproteins complemented HCV virus production in HCV transfected 293T/miR-122 cells, albeit with significantly lower efficacy compared with ApoE. In contrast, ApoD expression did not support production of infectious HCV. Specific infectivity of released particles complemented with ApoA family members was significantly lower compared with ApoE. Moreover, the ratio of extracellular to intracellular infectious virus was significantly higher for ApoE compared to ApoA2 and ApoC3. Since apolipoproteins complementing HCV virus production share amphipathic alpha helices as common structural features we altered the two alpha helices of ApoC1. Helix breaking mutations in both ApoC1 helices impaired virus assembly highlighting a critical role of alpha helices in apolipoproteins supporting HCV assembly. In summary, various liver expressed apolipoproteins with amphipathic alpha helices complement HCV virus production in human non liver cells. Differences in the efficiency of virus assembly, the specific infectivity of released particles, and the ratio between extracellular and intracellular infectivity point to distinct characteristics of these apolipoproteins that influence HCV assembly and cell entry. This will guide future research to precisely pinpoint how apolipoproteins function during virus assembly and cell entry.

Several Human Liver Cell Expressed Apolipoproteins Complement HCV Virus Production with Varying Efficacy Conferring Differential Specific Infectivity to Released Viruses

PubMed Central

Doepke, Mandy; Vieyres, Gabrielle; Todt, Daniel; Wölk, Benno; Vondran, Florian W. R.; Geffers, Robert; Lauber, Chris; Kaderali, Lars; Penin, François; Pietschmann, Thomas

2015-01-01

Apolipoprotein E (ApoE), an exchangeable apolipoprotein, is necessary for production of infectious Hepatitis C virus (HCV) particles. However, ApoE is not the only liver-expressed apolipoprotein and the role of other apolipoproteins for production of infectious HCV progeny is incompletely defined. Therefore, we quantified mRNA expression of human apolipoproteins in primary human hepatocytes. Subsequently, cDNAs encoding apolipoproteins were expressed in 293T/miR-122 cells to explore if they complement HCV virus production in cells that are non-permissive due to limiting endogenous levels of human apolipoproteins. Primary human hepatocytes expressed high mRNA levels of ApoA1, A2, C1, C3, E, and H. ApoA4, A5, B, D, F, J, L1, L2, L3, L4, L6, M, and O were expressed at intermediate levels, and C2, C4, and L5 were not detected. All members of the ApoA and ApoC family of lipoproteins complemented HCV virus production in HCV transfected 293T/miR-122 cells, albeit with significantly lower efficacy compared with ApoE. In contrast, ApoD expression did not support production of infectious HCV. Specific infectivity of released particles complemented with ApoA family members was significantly lower compared with ApoE. Moreover, the ratio of extracellular to intracellular infectious virus was significantly higher for ApoE compared to ApoA2 and ApoC3. Since apolipoproteins complementing HCV virus production share amphipathic alpha helices as common structural features we altered the two alpha helices of ApoC1. Helix breaking mutations in both ApoC1 helices impaired virus assembly highlighting a critical role of alpha helices in apolipoproteins supporting HCV assembly. In summary, various liver expressed apolipoproteins with amphipathic alpha helices complement HCV virus production in human non liver cells. Differences in the efficiency of virus assembly, the specific infectivity of released particles, and the ratio between extracellular and intracellular infectivity point to distinct characteristics of these apolipoproteins that influence HCV assembly and cell entry. This will guide future research to precisely pinpoint how apolipoproteins function during virus assembly and cell entry. PMID:26226615

Cascades of energy and helicity in axisymmetric turbulence

NASA Astrophysics Data System (ADS)

Qu, Bo; Naso, Aurore; Bos, Wouter J. T.

2018-01-01

A spectral analysis of strictly axisymmetric turbulence is performed. Both freely decaying and statistically steady flows are considered. In helical flows we identify a dual cascade, where energy is transferred towards the large scales and helicity to the smallest ones. It is shown that even in the absence of net helicity, a dual cascade persists, transferring energy backward and positively and negatively polarized helicity fluctuations forward.

A synthetic diagnostic for beam emission spectroscopy in the helically symmetric experiment stellarator

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

Dobbins, T. J., E-mail: tdobbins@wisc.edu; Kumar, S. T. A.; Anderson, D. T.

The Helically Symmetric Experiment (HSX) has a number of active spectroscopy diagnostics. Due to the relatively large beam width compared to the plasma minor radius, it is difficult to achieve good spatial resolution at the core of the HSX plasma. This is due to the fact that the optical sightline cuts through many flux surfaces with varying field vectors within the beam. In order to compare the experimental results with theoretical models it is important to accurately model the beam width effects. A synthetic diagnostic has been developed for this purpose. This synthetic diagnostic calculates the effect of spot sizemore » and beam width on the measurements of quantities of interest, including radial electric field, flow velocity, and Stark polarization.« less

A synthetic diagnostic for beam emission spectroscopy in the helically symmetric experiment stellarator

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

Dobbins, T. J.; Kumar, S. T. A.; Anderson, D. T.

The Helically Symmetric Experiment (HSX) has a number of active spectroscopy diagnostics. Due to the relatively large beam width compared to the plasma minor radius, it is difficult to achieve good spatial resolution at the core of the HSX plasma. This is due to the fact that the optical sightline cuts through many flux surfaces with varying field vectors within the beam. It is important to accurately model the beam width effects in order to compare the experimental results with theoretical models. We've developed a synthetic diagnostic for this purpose. This synthetic diagnostic calculates the effect of spot size andmore » beam width on the measurements of quantities of interest, including radial electric field, flow velocity, and Stark polarization.« less

A synthetic diagnostic for beam emission spectroscopy in the helically symmetric experiment stellarator

DOE PAGES

Dobbins, T. J.; Kumar, S. T. A.; Anderson, D. T.

2016-08-03

The Helically Symmetric Experiment (HSX) has a number of active spectroscopy diagnostics. Due to the relatively large beam width compared to the plasma minor radius, it is difficult to achieve good spatial resolution at the core of the HSX plasma. This is due to the fact that the optical sightline cuts through many flux surfaces with varying field vectors within the beam. It is important to accurately model the beam width effects in order to compare the experimental results with theoretical models. We've developed a synthetic diagnostic for this purpose. This synthetic diagnostic calculates the effect of spot size andmore » beam width on the measurements of quantities of interest, including radial electric field, flow velocity, and Stark polarization.« less

Experimental and predicted cavitation performance of an 80.6 deg helical inducer in high temperature water

NASA Technical Reports Server (NTRS)

Kovich, G.

1972-01-01

The cavitating performance of a stainless steel 80.6 degree flat-plate helical inducer was investigated in water over a range of liquid temperatures and flow coefficients. A semi-empirical prediction method was used to compare predicted values of required net positive suction head in water with experimental values obtained in water. Good agreement was obtained between predicted and experimental data in water. The required net positive suction head in water decreased with increasing temperature and increased with flow coefficient, similar to that observed for a like inducer in liquid hydrogen.

COSMIC-RAY PITCH-ANGLE SCATTERING IN IMBALANCED MHD TURBULENCE SIMULATIONS

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

Weidl, Martin S.; Jenko, Frank; Teaca, Bogdan

2015-09-20

Pitch-angle scattering rates for cosmic-ray particles in MHD simulations with imbalanced turbulence are calculated for fully evolving electromagnetic turbulence. We compare with theoretical predictions derived from the quasilinear theory of cosmic-ray diffusion for an idealized slab spectrum and demonstrate how cross helicity affects the shape of the pitch-angle diffusion coefficient. Additional simulations in evolving magnetic fields or static field configurations provide evidence that the scattering anisotropy in imbalanced turbulence is not primarily due to coherence with propagating Alfvén waves, but an effect of the spatial structure of electric fields in cross-helical MHD turbulence.

Measurements of Magnetic Helicity within Two Interacting Flux Ropes

NASA Astrophysics Data System (ADS)

Dehaas, Timothy; Gekelman, Walter

2016-10-01

Magnetic helicity (HM) has become a useful tool in the exploration of astrophysical plasmas. Its conservation in the MHD limit (and even some fluid approaches) constrains the global behavior of large plasma structures. One such astrophysical structure is a magnetic flux rope: a rope-like, current-carrying plasma embedded in an external magnetic field. Bundles of these ropes are commonly observed extending from the solar surface and can be found in the near-earth environment. In this well-diagnosed experiment (3D measurements of ne, Te, Vp, B, J, E, uflow) , two magnetic flux ropes were generated in the Large Plasma Device at UCLA. These ropes were driven kink-unstable, commencing complex motion. As they interact, helicity conservation is broken in regions of reconnection, turbulence, and instabilities. The changes in helicity can be visualized as 1) the transport of helicity (ϕB +E × A) and 2) the dissipation of the helicity (-2EB). Magnetic helicity is observed to have a negative sign and its counterpart, cross helicity, a positive one. These qualities oscillate 8% peak-to-peak. As the ropes move and the topology of the field lines change, a quasi-separatrix layer (QSL) is formed. The volume averaged HM and the largest value of Q both oscillate but not in phase. In addition to magnetic helicity, similar quantities such as self-helicity, mutual-helicity, vorticity, and canonical helicity are derived and will be presented. This work is supported by LANL-UC research Grant and done at the Basic Plasma Science Facility, which is funded by DOE and NSF.

Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides.

PubMed

Beck, David A C; Armen, Roger S; Daggett, Valerie

2005-01-18

The correct treatment of van der Waals and electrostatic nonbonded interactions in molecular force fields is essential for performing realistic molecular dynamics (MD) simulations of solvated polypeptides. The most computationally tractable treatment of nonbonded interactions in MD utilizes a spherical distance cutoff (typically, 8-12 A) to reduce the number of pairwise interactions. In this work, we assess three spherical atom-based cutoff approaches for use with all-atom explicit solvent MD: abrupt truncation, a CHARMM-style electrostatic shift truncation, and our own force-shifted truncation. The chosen system for this study is an end-capped 17-residue alanine-based alpha-helical peptide, selected because of its use in previous computational and experimental studies. We compare the time-averaged helical content calculated from these MD trajectories with experiment. We also examine the effect of varying the cutoff treatment and distance on energy conservation. We find that the abrupt truncation approach is pathological in its inability to conserve energy. The CHARMM-style shift truncation performs quite well but suffers from energetic instability. On the other hand, the force-shifted spherical cutoff method conserves energy, correctly predicts the experimental helical content, and shows convergence in simulation statistics as the cutoff is increased. This work demonstrates that by using proper and rigorous techniques, it is possible to correctly model polypeptide dynamics in solution with a spherical cutoff. The inherent computational advantage of spherical cutoffs over Ewald summation (and related) techniques is essential in accessing longer MD time scales.

Fan-shaped complete block on helical tomotherapy for esophageal cancer: a phantom study.

PubMed

Chang, Chiu-Han; Mok, Greta S P; Shueng, Pei-Wei; Yeh, Hsin-Pei; Shiau, An-Cheng; Tien, Hui-Ju; Lin, Chi-Ta; Wu, Tung-Hsin

2015-01-01

Radiation pneumonitis (RP) is a common complication for radiotherapy of esophageal cancer and is associated with the low dose irradiated lung volume. This study aims to reduce the mean lung dose (MLD) and the relative lung volume at 20 Gy (V 20) and at low dose region using various designs of the fan-shaped complete block (FSCB) in helical tomotherapy. Hypothetical esophageal tumor was delineated on an anthropomorphic phantom. The FSCB was defined as the fan-shaped radiation restricted area located in both lungs. Seven treatment plans were performed with nonblock design and FSCB with different fan angles, that is, from 90° to 140°, with increment of 10°. The homogeneous index, conformation number, MLD, and the relative lung volume receiving more than 5, 10, 15, and 20 Gy (V 5, V 10, V 15, and V 20) were determined for each treatment scheme. There was a substantial reduction in the MLD, V 5, V 10, V 15, and V 20 when using different types of FSCB as compared to the nonblock design. The reduction of V 20, V 15, V 10, and V 5 was 6.3%-8.6%, 16%-23%, 42%-57%, and 42%-66% for FSCB 90°-140°, respectively. The use of FSCB in helical tomotherapy is a promising method to reduce the MLD, V 20, and relative lung volume in low dose region, especially in V 5 and V 10 for esophageal cancer.

Numerical simulation of helical flow in a cylindrical channel

NASA Astrophysics Data System (ADS)

Vasiliev, A.; Sukhanovskii, A.; Stepanov, R.

2017-06-01

Numerical simulation of the helical flow in a cylindrical channel with diverter was carried out using open-source software OpenFOAM Extend 4.0. The velocity, vorticity and helicity density distributions were analyzed. It was shown that azimithal contribution of helicity is negative near the wall and positive in the center. In opposite axial helicity contribution is negative in the center and positive near the wall. Analysis of helicity of non-axisymmetric part of the flow showed that it has substantial values near the diverter but than rapidly decreases with y (axial coordinate) and further downstream it can be neglected. Dependencies of integrated values of azimuthal Hϕ and axial Hy contributions of helicity density on y show a remarkable quantitative similarity. It was found that integral values of Hϕ and Hy are negative for all y. Magnitudes of Hϕ and Hy decrease after the diverter up to y ≈ 70 mm and after that monotonically increase. The flow behind the diverter is characterized by substantial amount of helicity and can be used as a helicity generator.

Dynamics and allostery of the ionotropic glutamate receptors and the ligand binding domain.

PubMed

Tobi, Dror

2016-02-01

The dynamics of the ligand-binding domain (LBD) and the intact ionotropic glutamate receptor (iGluR) were studied using Gaussian Network Model (GNM) analysis. The dynamics of LBDs with various allosteric modulators is compared using a novel method of multiple alignment of GNM modes of motion. The analysis reveals that allosteric effectors change the dynamics of amino acids at the upper lobe interface of the LBD dimer as well as at the hinge region between the upper- and lower- lobes. For the intact glutamate receptor the analysis show that the clamshell-like movement of the LBD upper and lower lobes is coupled to the bending of the trans-membrane domain (TMD) helices which may open the channel pore. The results offer a new insight on the mechanism of action of allosteric modulators on the iGluR and support the notion of TMD helices bending as a possible mechanism for channel opening. In addition, the study validates the methodology of multiple GNM modes alignment as a useful tool to study allosteric effect and its relation to proteins dynamics. © 2015 Wiley Periodicals, Inc.

Inhomogeneous helicity effect in the solar angular-momentum transport

NASA Astrophysics Data System (ADS)

Yokoi, Nobumitsu

2017-04-01

Coupled with mean absolute vorticity Ω∗ (rotation and mean relative vorticity), inhomogeneous turbulent helicity is expected to contribute to the generation of global flow structure against the linear and angular momentum mixing due to turbulent or eddy viscosity. This inhomogeneous helicity effect was originally derived in Yokoi & Yoshizawa (1993) [1], and recently has been validated by direct numerical simulations (DNSs) of rotating helical turbulence [2]. Turbulence effect enters the mean-vorticity equation through the turbulent vortexmotive force ⟨u'×ω'⟩ [u': velocity fluctuation, ω'(= ∇× u'): vorticity fluctuation], which is the vorticity counterpart of the electromotive force ⟨u'× b'⟩ (b': magnetic fluctuation) in the mean magnetic-field induction. The mean velocity induction δU is proportional to the vortexmotive force. According to the theoretical result [1,2], it is expressed as δU = -νT∇×Ω∗-ηT(∇2H)Ω∗, where ηT is the transport coefficient, H = ⟨u'ṡω'⟩ the turbulent helicity, and Ω∗ the mean absolute vorticity. The first term corresponds to the enhanced diffusion due to turbulent viscosity νT. The second term expresses the large-scale flow generation due to inhomogeneous helicity. Since helicity is self-generated in rotating stratified turbulence [3], an inhomogeneous helicity distribution is expected to exist in the solar convection zone. A rising flow with expansion near the surface of the Sun generates a strongly negative helicity there [4]. This spatial distribution of helicity would lead to a positive Laplacian of turbulent helicity (∇2H > 0) in the subsurface layer of the Sun. In the combination with the large-scale vorticity associated with the meridional circulation, the inhomogeneous helicity effect works for accelerating the mean velocity in the azimuthal direction. The relevance of this inhomogeneous helicity effect in the solar convection zone is discussed further. References [1] Yokoi, N. and Yoshizawa, A., "Statistical analysis of the effects of helicity in inhomogeneous turbulence," Phys. Fluids A, 5, 464-477 (1993). [2] Yokoi, N. and Brandenburg, A., "Large-scale flow generation by inhomogeneous helicity," Phys. Rev. E, 93, 033125-1-14 (2016). [3] Marino, R., Mininni, P., Rosenberg, D., and Pouquet, A., "Emergence of helicity in rotating stratified turbulence," Phys. Rev. E, 87, 033016-1-9 (2013). [4] Duarte, L. D. V., Wicht, J., Browning, M. K., and Gastine, T., "Helicity inversion in spherical convection as a means for equatorward dynamo wave propagation," Mon. Not. Roy. Astron. Soc. 456, 1708-1722 (2016).

Influence of gantry rotation time and scan mode on image quality in ultra-high-resolution CT system.

PubMed

Honda, Osamu; Yanagawa, Masahiro; Hata, Akinori; Kikuchi, Noriko; Miyata, Tomo; Tsukagoshi, Shinsuke; Uranishi, Ayumi; Tomiyama, Noriyuki

2018-06-01

To investigate the image quality of helical scan (HS) mode and non-helical scan (non-HS) mode on ultra-high-resolution CT in different gantry rotation time. non-HS with 0.35 s/rot (non-HS200 mA/0.35 s). Three observers compared each non-HS image with HS image, and scored non-HS images by using 3-point scale, paying attention to normal findings, abnormal findings, noise, streak artifact, and overall image quality. Statistical analysis was performed with Steel-Dwass test. Overall image quality (score: 2.45) and noise (score: 2.42) of non-HS 200 mA/1.5s was statistically best (p < 0.0005). Overall Image quality and noise of non-HS200 mA/0.75 s (score: 2.0) was comparable to that of HS200 mA/1.5 s. CTDIvol of HS200 mA/1.5 s is 23.2 mGy. CTDIvol of non-HS200 mA/1.5 s, non-HS200 mA/0.75 s, non-HS200 mA/0.35 s is 19.2 mGy, 9.8 mGy, 4.7 mGy. Overall image quality and noise of non-helical scan is better than that of helical scan in the same rotation time. Overall Image quality of non-HS200 mA/0.75 s is comparable to that of HS200 mA/1.5 s, though the radiation dose of non-HS200 mA/0.75 s is lower than that of HS200 mA/1.5 s. Copyright © 2018 Elsevier B.V. All rights reserved.

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

[The electron microscopic findings of helicoid bacteria lining the mucosa of the cecum in guinea pigs].

PubMed

Raygoza-Anaya, M; Bondarenko, V M; Mora-Galindo, H; González-Robles, A

1991-08-01

This study has revealed that helical bacteria inhabiting the mucous membrane of the cecum of guinea pigs are localized in the parietal zone of the epithelium and can be detected as biological film consisting of many microcolonies. Helical bacteria are attached to the epithelium by insertion of one of the ends of an eukaryotic cell into the space between microvilli without damaging epithelial cells and their microvilli. Helical bacteria have been found to use the "anchor" type of attachment to the epithelium, which ensures the stability of their high population level in the biotope. These microorganisms appear on the mucous membrane of the epithelium, starting from day 15 of the life of guinea pigs. At the period of the transition of suckling guinea pigs to independent nourishment the population of helical bacteria is partially suppressed due to the appearance of bacillary and filamentous forms of bacteria, but later, after the adaptation of the animals to their diet, helical bacteria become normal resident microflora which forms biofilm covering large areas of the mucous membrane and the entrances of crypts of Lieberkühn.

Tile-based self-assembly of a triple-helical polysaccharide into cell wall-like mesoporous nanocapsules.

PubMed

Wu, Chaoxi; Wang, Xiaoying; Wang, Jianjing; Zhang, Zhen; Wang, Zhiping; Wang, Yifei; Tang, Shunqing

2017-07-20

Tile-based self-assembly is a robust system in the construction of three-dimensional DNA nanostructures but it has been rarely applied to other helical biopolymers. β-Glucan is an immunoactive natural polymer which exists in a triple helical conformation. Herein, we report that β-glucan, after modification using two types of short chain acyl groups, can self-assemble into tiles with inactivated sticky ends at the interface of two solvents. These tiles consist of a single layer of helices laterally aligned, and the sticky ends can be activated when a few acyl groups at the ends are removed; these tiles can further pack into mesoporous nanocapsules, in a similar process as the sticky DNA tiles pack into complex polyhedral nano-objects. These nanocapsules were found to have targeted effects to antigen presenting cells in a RAW264.7 cell model. Our study suggests that tile-based self-assembly can be a general strategy for helical biopolymers, and on fully exploiting this strategy, various new functional nanostructures will become accessible in the future.

Paired helical filaments of inclusion-body myositis muscle contain RNA and survival motor neuron protein.

PubMed

Broccolini, A; Engel, W K; Alvarez, R B; Askanas, V

2000-04-01

Sporadic inclusion-body myositis (s-IBM) is the most common progressive muscle disease of older persons. Pathologically, the muscle biopsy manifests various degrees of inflammation and specific vacuolar degeneration of muscle fibers characterized by paired helical filaments (PHFs) composed of phosphorylated tau. IBM vacuolated fibers also contain accumulations of several other Alzheimer-characteristic proteins. Molecular mechanisms leading to formation of the PHFs and accumulations of proteins in IBM muscle are not known. We report that the abnormal muscle fibers of IBM contained (i) acridine-orange-positive RNA inclusions that colocalized with the immunoreactivity of phosphorylated tau and (ii) survival motor neuron protein immunoreactive inclusions, which by immuno-electron microscopy were confined to paired helical filaments. This study demonstrates two novel components of the IBM paired helical filaments, which may lead to better understanding of their pathogenesis.

Faraday signature of magnetic helicity from reduced depolarization

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

Brandenburg, Axel; Stepanov, Rodion

2014-05-10

Using one-dimensional models, we show that a helical magnetic field with an appropriate sign of helicity can compensate the Faraday depolarization resulting from the superposition of Faraday-rotated polarization planes from a spatially extended source. For radio emission from a helical magnetic field, the polarization as a function of the square of the wavelength becomes asymmetric with respect to zero. Mathematically speaking, the resulting emission occurs then either at observable or at unobservable (imaginary) wavelengths. We demonstrate that rotation measure (RM) synthesis allows for the reconstruction of the underlying Faraday dispersion function in the former case, but not in the latter.more » The presence of positive magnetic helicity can thus be detected by observing positive RM in highly polarized regions in the sky and negative RM in weakly polarized regions. Conversely, negative magnetic helicity can be detected by observing negative RM in highly polarized regions and positive RM in weakly polarized regions. The simultaneous presence of two magnetic constituents with opposite signs of helicity is shown to possess signatures that can be quantified through polarization peaks at specific wavelengths and the gradient of the phase of the Faraday dispersion function. Similar polarization peaks can tentatively also be identified for the bi-helical magnetic fields that are generated self-consistently by a dynamo from helically forced turbulence, even though the magnetic energy spectrum is then continuous. Finally, we discuss the possibility of detecting magnetic fields with helical and non-helical properties in external galaxies using the Square Kilometre Array.« less

Magnetic field generation by pointwise zero-helicity three-dimensional steady flow of an incompressible electrically conducting fluid

NASA Astrophysics Data System (ADS)

Rasskazov, Andrey; Chertovskih, Roman; Zheligovsky, Vladislav

2018-04-01

We introduce six families of three-dimensional space-periodic steady solenoidal flows, whose kinetic helicity density is zero at any point. Four families are analytically defined. Flows in four families have zero helicity spectrum. Sample flows from five families are used to demonstrate numerically that neither zero kinetic helicity density nor zero helicity spectrum prohibit generation of large-scale magnetic field by the two most prominent dynamo mechanisms: the magnetic α -effect and negative eddy diffusivity. Our computations also attest that such flows often generate small-scale field for sufficiently small magnetic molecular diffusivity. These findings indicate that kinetic helicity and helicity spectrum are not the quantities controlling the dynamo properties of a flow regardless of whether scale separation is present or not.

Predictive Power-balance Modeling of PEGASUS and NSTX-U Local Helicity Injection Discharges

NASA Astrophysics Data System (ADS)

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

2013-10-01

Local helicity injection (LHI) with outer poloidal-field (PF) induction for solenoid-free startup is being studied on PEGASUS, reaching Ip <= 0 . 175 MA with 6 kA of injected current. A lumped-parameter circuit model for predicting the performance of LHI initiated plasmas is under development. The model employs energy and helicity balance, and includes applied PF ramping and the inductive effects of shape evolution. Low- A formulations for both the plasma external inductance and a uniform equilibrium-field are used to estimate inductive voltages. PEGASUS LHI plasmas are created near the outboard injectors with aspect ratio (A) ~ 5-6.5 and grow inward to fill the confinement region at A <= 1 . 3 . Initial results match experimental Ip (t) trajectories within 15 kA with a prescribed geometry evolution. Helicity injection is the largest driving term in the initial phase, but in the later phase is reduced to 20-45% of the total drive as PF induction and decreasing plasma inductance become dominant. In contrast, attaining ~1 MA non-solenoidal startup via LHI on NSTX-U will require operation in the regime where helicity injection drive exceeds inductive and geometric changes at full size. A large-area multi-injector array will increase available helicity injection by 3-4 times and allow exploration of this helicity-dominated regime at Ip ~ 0 . 3 MA in PEGASUS. Comparison of model predictions with time-evolving magnetic equilibria is in progress for model validation. Work supported by US DOE Grant DE-FG02-96ER54375.

Assembly of mesoscale helices with near-unity enantiomeric excess and light-matter interactions for chiral semiconductors.

PubMed

Feng, Wenchun; Kim, Ji-Young; Wang, Xinzhi; Calcaterra, Heather A; Qu, Zhibei; Meshi, Louisa; Kotov, Nicholas A

2017-03-01

Semiconductors with chiral geometries at the nanoscale and mesoscale provide a rich materials platform for polarization optics, photocatalysis, and biomimetics. Unlike metallic and organic optical materials, the relationship between the geometry of chiral semiconductors and their chiroptical properties remains, however, vague. Homochiral ensembles of semiconductor helices with defined geometries open the road to understanding complex relationships between geometrical parameters and chiroptical properties of semiconductor materials. We show that semiconductor helices can be prepared with an absolute yield of ca 0.1% and an enantiomeric excess (e.e.) of 98% or above from cysteine-stabilized cadmium telluride nanoparticles (CdTe NPs) dispersed in methanol. This high e.e. for a spontaneously occurring chemical process is attributed to chiral self-sorting based on the thermodynamic preference of NPs to assemble with those of the same handedness. The dispersions of homochiral self-assembled helices display broadband visible and near-infrared (Vis-NIR) polarization rotation with anisotropy ( g ) factors approaching 0.01. Calculated circular dichroism (CD) spectra accurately reproduced experimental CD spectra and gave experimentally validated spectral predictions for different geometrical parameters enabling de novo design of chiroptical semiconductor materials. Unlike metallic, ceramic, and polymeric helices that serve predominantly as scatterers, chiroptical properties of semiconductor helices have nearly equal contribution of light absorption and scattering, which is essential for device-oriented, field-driven light modulation. Deconstruction of a helix into a series of nanorods provides a simple model for the light-matter interaction and chiroptical activity of helices. This study creates a framework for further development of polarization-based optics toward biomedical applications, telecommunications, and hyperspectral imaging.

Helical vortices generated by flapping wings of bumblebees

NASA Astrophysics Data System (ADS)

Engels, Thomas; Kolomenskiy, Dmitry; Schneider, Kai; Farge, Marie; Lehmann, Fritz-Olaf; Sesterhenn, Jörn

2018-02-01

High resolution direct numerical simulations of rotating and flapping bumblebee wings are presented and their aerodynamics is studied focusing on the role of leading edge vortices and the associated helicity production. We first study the flow generated by only one rotating bumblebee wing in circular motion with 45◦ angle of attack. We then consider a model bumblebee flying in a numerical wind tunnel, which is tethered and has rigid wings flapping with a prescribed generic motion. The inflow condition of the wind varies from laminar to strongly turbulent regimes. Massively parallel simulations show that inflow turbulence does not significantly alter the wings’ leading edge vortex, which enhances lift production. Finally, we focus on studying the helicity of the generated vortices and analyze their contribution at different scales using orthogonal wavelets.

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.

Tire

NASA Technical Reports Server (NTRS)

Benzing, II, James Alfred (Inventor); Kish, James Christopher (Inventor); Asnani, Vivake Manohar (Inventor)

2012-01-01

A tire includes a plurality of helical springs. Each helical spring includes a first end portion, a second end portion, and an arching middle portion. Each helical spring is interlaced with at least one other helical spring thereby forming a laced toroidal structure extending about an entire circumference of the tire.

Helical bottleneck effect in 3D homogeneous isotropic turbulence

NASA Astrophysics Data System (ADS)

Stepanov, Rodion; Golbraikh, Ephim; Frick, Peter; Shestakov, Alexander

2018-02-01

We present the results of modelling the development of homogeneous and isotropic turbulence with a large-scale source of energy and a source of helicity distributed over scales. We use the shell model for numerical simulation of the turbulence at high Reynolds number. The results show that the helicity injection leads to a significant change in the behavior of the energy and helicity spectra in scales larger and smaller than the energy injection scale. We suggest the phenomenology for direct turbulent cascades with the helicity effect, which reduces the efficiency of the spectral energy transfer. Therefore the energy is accumulated and redistributed so that non-linear interactions will be sufficient to provide a constant energy flux. It can be interpreted as the ‘helical bottleneck effect’ which, depending on the parameters of the injection helicity, reminds one of the well-known bottleneck effect at the end of inertial range. Simulations which included the infrared part of the spectrum show that the inverse cascade hardly develops under distributed helicity forcing.

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

Lello, Louis; Boyanovsky, Daniel; Pisarski, Robert D.

Here, in the standard model extended with a seesaw mass matrix, we study the production of sterile neutrinos from the decay of vector bosons at temperatures near the masses of the electroweak bosons. We derive a general quantum kinetic equation for the production of sterile neutrinos and their effective mixing angles, which is applicable over a wide range of temperature, to all orders in interactions of the standard model and to leading order in a small mixing angle for the neutrinos. We emphasize the relation between the production rate and Landau damping at one-loop order and show that production rates and effective mixing angles depend sensitively upon the neutrino’s helicity. Sterile neutrinos with positive helicity interact more weakly with the medium than those with negative helicity, and their effective mixing angle is not modified significantly. Negative helicity states couple more strongly to the vector bosons, but their mixing angle is strongly suppressed by the medium. Consequently, if the mass of the sterile neutrino is ≲ 8.35 MeV , there are fewer states with negative helicity produced than those with positive helicity. There is an Mikheyev-Smirnov-Wolfenstein-type resonance in the absence of lepton asymmetry, but due to screening by the damping rate, the production rate is not enhanced. Sterile neutrinos with negative helicity freeze out at Tmore » $$-\\atop{f}$$ ≃ 5 GeV , whereas positive helicity neutrinos freeze out at T$$+\\atop{f}$$≃ 8 GeV , with both distributions far from thermal. As the temperature decreases, due to competition between a decreasing production rate and an increasing mixing angle, the distribution function for states with negative helicity is broader in momentum and hotter than that for those with positive helicity. Sterile neutrinos produced via vector boson decay do not satisfy the abundance, lifetime, and cosmological constraints to be the sole dark matter component in the Universe. Massive sterile neutrinos produced via vector boson decay might solve the 7Li problem, albeit at the very edge of the possible parameter space. A heavy sterile neutrino with a mass of a few MeV could decay into light sterile neutrinos, of a few keV in mass, that contribute to warm dark matter. In conclusion, we argue that heavy sterile neutrinos with lifetime ≤1/H 0 reach local thermodynamic equilibrium.« less

Production of heavy sterile neutrinos from vector boson decay at electroweak temperatures

NASA Astrophysics Data System (ADS)

Lello, Louis; Boyanovsky, Daniel; Pisarski, Robert D.

2017-02-01

In the standard model extended with a seesaw mass matrix, we study the production of sterile neutrinos from the decay of vector bosons at temperatures near the masses of the electroweak bosons. We derive a general quantum kinetic equation for the production of sterile neutrinos and their effective mixing angles, which is applicable over a wide range of temperature, to all orders in interactions of the standard model and to leading order in a small mixing angle for the neutrinos. We emphasize the relation between the production rate and Landau damping at one-loop order and show that production rates and effective mixing angles depend sensitively upon the neutrino's helicity. Sterile neutrinos with positive helicity interact more weakly with the medium than those with negative helicity, and their effective mixing angle is not modified significantly. Negative helicity states couple more strongly to the vector bosons, but their mixing angle is strongly suppressed by the medium. Consequently, if the mass of the sterile neutrino is ≲8.35 MeV , there are fewer states with negative helicity produced than those with positive helicity. There is an Mikheyev-Smirnov-Wolfenstein-type resonance in the absence of lepton asymmetry, but due to screening by the damping rate, the production rate is not enhanced. Sterile neutrinos with negative helicity freeze out at Tf-≃5 GeV , whereas positive helicity neutrinos freeze out at Tf+≃8 GeV , with both distributions far from thermal. As the temperature decreases, due to competition between a decreasing production rate and an increasing mixing angle, the distribution function for states with negative helicity is broader in momentum and hotter than that for those with positive helicity. Sterile neutrinos produced via vector boson decay do not satisfy the abundance, lifetime, and cosmological constraints to be the sole dark matter component in the Universe. Massive sterile neutrinos produced via vector boson decay might solve the 7Li problem, albeit at the very edge of the possible parameter space. A heavy sterile neutrino with a mass of a few MeV could decay into light sterile neutrinos, of a few keV in mass, that contribute to warm dark matter. We argue that heavy sterile neutrinos with lifetime ≤1 /H0 reach local thermodynamic equilibrium.

Production of heavy sterile neutrinos from vector boson decay at electroweak temperatures

DOE PAGES

Lello, Louis; Boyanovsky, Daniel; Pisarski, Robert D.

2017-02-22

Here, in the standard model extended with a seesaw mass matrix, we study the production of sterile neutrinos from the decay of vector bosons at temperatures near the masses of the electroweak bosons. We derive a general quantum kinetic equation for the production of sterile neutrinos and their effective mixing angles, which is applicable over a wide range of temperature, to all orders in interactions of the standard model and to leading order in a small mixing angle for the neutrinos. We emphasize the relation between the production rate and Landau damping at one-loop order and show that production rates and effective mixing angles depend sensitively upon the neutrino’s helicity. Sterile neutrinos with positive helicity interact more weakly with the medium than those with negative helicity, and their effective mixing angle is not modified significantly. Negative helicity states couple more strongly to the vector bosons, but their mixing angle is strongly suppressed by the medium. Consequently, if the mass of the sterile neutrino is ≲ 8.35 MeV , there are fewer states with negative helicity produced than those with positive helicity. There is an Mikheyev-Smirnov-Wolfenstein-type resonance in the absence of lepton asymmetry, but due to screening by the damping rate, the production rate is not enhanced. Sterile neutrinos with negative helicity freeze out at Tmore » $$-\\atop{f}$$ ≃ 5 GeV , whereas positive helicity neutrinos freeze out at T$$+\\atop{f}$$≃ 8 GeV , with both distributions far from thermal. As the temperature decreases, due to competition between a decreasing production rate and an increasing mixing angle, the distribution function for states with negative helicity is broader in momentum and hotter than that for those with positive helicity. Sterile neutrinos produced via vector boson decay do not satisfy the abundance, lifetime, and cosmological constraints to be the sole dark matter component in the Universe. Massive sterile neutrinos produced via vector boson decay might solve the 7Li problem, albeit at the very edge of the possible parameter space. A heavy sterile neutrino with a mass of a few MeV could decay into light sterile neutrinos, of a few keV in mass, that contribute to warm dark matter. In conclusion, we argue that heavy sterile neutrinos with lifetime ≤1/H 0 reach local thermodynamic equilibrium.« less

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

PubMed

Zhang, Qi-Yi

2017-02-01

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

Toda-Lattice Solitons in α-Helical Proteins

NASA Astrophysics Data System (ADS)

Yomosa, Shigeo

1984-10-01

We propose a theory of Toda-lattice soliton in α-helical proteins which enables us to elucidate the molecular dynamics of muscle contraction. One-dimensional chain of peptide groups jointed together by H-bonds, which stabilizes α-helical structure of proteins, can be regarded as a Toda-lattice where the potential of H-bonding interaction between peptide groups has a remarkable nonlinearity. By using the results of theoretical studies for Toda-lattice soliton and for the initial value problem, we can describe the molecular mechanism of the transformation of the chemical energy to the mechanical work in the process of the muscle contraction.

Oligoalanine helical callipers for cell penetration.

PubMed

Pazo, Marta; Juanes, Marisa; Lostalé-Seijo, Irene; Montenegro, Javier

2018-06-04

Even for short peptides that are enriched in basic amino acids, the large chemical space that can be spanned by combinations of natural amino acids hinders the rational design of cell penetrating peptides. We here report on short oligoalanine scaffolds for the fine-tuning of peptide helicity in different media and the study of cell penetrating properties. This strategy allowed the extraction of the structure/activity features required for maximal membrane interaction and cellular penetration at minimal toxicity. These results confirmed oligoalanine helical callipers as optimal scaffolds for the rational design and the identification of cell penetrating peptides.

Chiral Organic Cages with a Triple-Stranded Helical Structure Derived from Helicene.

PubMed

Malik, Abaid Ullah; Gan, Fuwei; Shen, Chengshuo; Yu, Na; Wang, Ruibin; Crassous, Jeanne; Shu, Mouhai; Qiu, Huibin

2018-02-28

We report the use of helicene with an intrinsic helical molecular structure to prepare covalent organic cages via imine condensation. The organic cages revealed a [3+2]-type architecture containing a triple-stranded helical structure with three helicene units arranged in a propeller-like fashion with the framework integrally twisted. Such structural chirality was retained upon dissolution in organic solvents, as indicated by a strong diastereotopy effect in proton NMR and unique Cotton effects in circular dichroism spectra. Further study on chiral adsorption showed that the chiral organic cages possess considerable enantioselectivity toward a series of aromatic racemates.

Experimental Study of the Influence of Speed and Load on Thermal Behavior of High-Speed Helical Gear Trains

NASA Technical Reports Server (NTRS)

Handschuh, R.; Kilmain, C.

2005-01-01

An experimental effort has been conducted on an aerospace-quality helical gear train to investigate the thermal behavior of the gear system as speed, load, and lubricant flow rate were varied. Temperature test data from a helical gear train at varying speeds and loads (to 5000 hp and 15000 rpm) was collected using thermocouple rakes and axial arrays. The instrumentation was able to capture the radial and axial expelled lubricant-air environment (fling-off lubricant) that is expelled during the gear meshing process. Effects of operational characteristics are presented.

Exploration of nucleoprotein α-MoRE and XD interactions of Nipah and Hendra viruses.

PubMed

Shang, Xu; Chu, Wenting; Chu, Xiakun; Xu, Liufang; Longhi, Sonia; Wang, Jin

2018-04-24

Henipavirus, including Hendra virus (HeV) and Nipah virus (NiV), is a newly discovered human pathogen genus. The nucleoprotein of Henipavirus contains an α-helical molecular recognition element (α-MoRE) that folds upon binding to the X domain (XD) of the phosphoprotein (P). In order to explore the conformational dynamics of free α-MoREs and the underlying binding-folding mechanism with XD, atomic force field-based and hybrid structure-based MD simulations were carried out. In our empirical force field-based simulations, characteristic structures and helicities of α-MoREs reveal the co-existence of partially structured and disordered conformations, as in the case of the well characterized cognate measles virus (MeV) α-MoRE. In spite of their overall similarity, the two α-MoREs display subtle helicity differences in their C-terminal region, but much different from that of MeV. For the α-MoRE/XD complexes, the results of our hybrid structure-based simulations provide the coupled binding-folding landscapes, and unveil a wide conformational selection mechanism at early binding stages, followed by a final induce-fit mechanism selection process. However, the HeV and NiV complexes have a lower binding barrier compared to that of MeV. Moreover, the HeV α-MoRE/XD complex shows much less coupling effects between binding and folding compared to that from both NiV and MeV. Our analysis revealed that contrary to NiV and MeV, the N- and C-terminal regions of the HeV α-MoRE maintains a low helicity also in the bound form.

Emergency department CT screening of patients with nontraumatic neurological symptoms referred to the posterior fossa: comparison of thin versus thick slice images.

PubMed

Kamalian, Shervin; Atkinson, Wendy L; Florin, Lauren A; Pomerantz, Stuart R; Lev, Michael H; Romero, Javier M

2014-06-01

Evaluation of the posterior fossa (PF) on 5-mm-thick helical CT images (current default) has improved diagnostic accuracy compared to 5-mm sequential CT images; however, 5-mm-thick images may not be ideal for PF pathology due to volume averaging of rapid changes in anatomy in the Z-direction. Therefore, we sought to determine if routine review of 1.25-mm-thin helical CT images has superior accuracy in screening for nontraumatic PF pathology. MRI proof of diagnosis was obtained within 6 h of helical CT acquisition for 90 consecutive ED patients with, and 88 without, posterior fossa lesions. Helical CT images were post-processed at 1.25 and 5-mm-axial slice thickness. Two neuroradiologists blinded to the clinical/MRI findings reviewed both image sets. Interobserver agreement and accuracy were rated using Kappa statistics and ROC analysis, respectively. Of the 90/178 (51 %) who were MR positive, 60/90 (66 %) had stroke and 30/90 (33 %) had other etiologies. There was excellent interobserver agreement (κ > 0.97) for both thick and thin slice assessments. The accuracy, sensitivity, and specificity for 1.25-mm images were 65, 44, and 84 %, respectively, and for 5-mm images were 67, 45, and 85 %, respectively. The diagnostic accuracy was not significantly different (p > 0.5). In this cohort of patients with nontraumatic neurological symptoms referred to the posterior fossa, 1.25-mm-thin slice CT reformatted images do not have superior accuracy compared to 5-mm-thick images. This information has implications on optimizing resource utilizations and efficiency in a busy emergency room. Review of 1.25-mm-thin images may help diagnostic accuracy only when review of 5-mm-thick images as current default is inconclusive.

Dynamics of zonal flows in helical systems.

PubMed

Sugama, H; Watanabe, T-H

2005-03-25

A theory for describing collisionless long-time behavior of zonal flows in helical systems is presented and its validity is verified by gyrokinetic-Vlasov simulation. It is shown that, under the influence of particles trapped in helical ripples, the response of zonal flows to a given source becomes weaker for lower radial wave numbers and deeper helical ripples while a high-level zonal-flow response, which is not affected by helical-ripple-trapped particles, can be maintained for a longer time by reducing their bounce-averaged radial drift velocity. This implies a possibility that helical configurations optimized for reducing neoclassical ripple transport can simultaneously enhance zonal flows which lower anomalous transport.

Accurate Cold-Test Model of Helical TWT Slow-Wave Circuits

NASA Technical Reports Server (NTRS)

Kory, Carol L.; Dayton, James A., Jr.

1997-01-01

Recently, a method has been established to accurately calculate cold-test data for helical slow-wave structures using the three-dimensional electromagnetic computer code, MAFIA. Cold-test parameters have been calculated for several helical traveling-wave tube (TWT) slow-wave circuits possessing various support rod configurations, and results are presented here showing excellent agreement with experiment. The helical models include tape thickness, dielectric support shapes and material properties consistent with the actual circuits. The cold-test data from this helical model can be used as input into large-signal helical TWT interaction codes making it possible, for the first time, to design a complete TWT via computer simulation.

Helical-Tip Needle for Transthoracic Percutaneous Image-Guided Biopsy of Lung Tumors: Results of a Pilot Prospective Comparative Study with a Standard Tru-Cut Needle

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

Veltri, Andrea, E-mail: andrea.veltri@unito.it; Busso, Marco; Sardo, Diego

PurposeTo prospectively evaluate feasibility and diagnostic performance of the 14-gauge helical-tip (Spirotome™, Cook{sup ®} Medical, Bloomington, USA) needle in transthoracic needle biopsy (TTNB) of lung lesions, compared to a conventional 18-gauge Tru-Cut needle.Materials and MethodsStudy was institutional review board approved, with informed consent obtained. Data from synchronous Spirotome and Tru-Cut image-guided TTNB of 20 consecutive patients with malignant peripheral lung tumors larger than 3 cm were enrolled for pathologic characterization and mutational analysis. Samples obtained with Spirotome and Tru-Cut needle were compared for fragmentation, length, weight, morphologic and immunohistochemistry typifying, tumor cellularity (TC) and DNA concentration.ResultsThe technical success rate for TTNBmore » with Spirotome was 100%, and no major complications occurred. Less fragmentation (mean 2 vs. 3 fragments, P = .418), greater weight (mean 13 vs. 8.5 mg, P = .027) and lower length (mean 10.2 vs. 12.6 mm, P = .174) were observed with Spirotome compared to Tru-Cut needle. Accuracy of Spirotome and Tru-Cut needle in defining cancer histotype was similar (90%). Absolute and relative TC (mean 42 vs. 38, 124 vs. 108/10HPF), and DNA concentration (mean 49.6 vs. 39.0 ng/μl) were higher with Spirotome compared to Tru-Cut needle, with no statistical significance (P = .787 and P = .140, respectively).Conclusions Percutaneous 14-gauge Spirotome TTNB of selected lesions is feasible and accurate. It provides adequate samples for diagnosis, comparable to 18-gauge Tru-Cut needle, with a higher amount of tumor tissue (weight, TC, DNA concentration) even in shorter samples.« less

Cruise noise of the 2/9th scale model of the Large-scale Advanced Propfan (LAP) propeller, SR-7A

NASA Technical Reports Server (NTRS)

Dittmar, James H.; Stang, David B.

1987-01-01

Noise data on the Large-scale Advanced Propfan (LAP) propeller model SR-7A were taken in the NASA Lewis Research Center 8 x 6 foot Wind Tunnel. The maximum blade passing tone noise first rises with increasing helical tip Mach number to a peak level, then remains the same or decreases from its peak level when going to higher helical tip Mach numbers. This trend was observed for operation at both constant advance ratio and approximately equal thrust. This noise reduction or, leveling out at high helical tip Mach numbers, points to the use of higher propeller tip speeds as a possible method to limit airplane cabin noise while maintaining high flight speed and efficiency. Projections of the tunnel model data are made to the full scale LAP propeller mounted on the test bed aircraft and compared with predictions. The prediction method is found to be somewhat conservative in that it slightly overpredicts the projected model data at the peak.

Cruise noise of the 2/9 scale model of the Large-scale Advanced Propfan (LAP) propeller, SR-7A

NASA Technical Reports Server (NTRS)

Dittmar, James H.; Stang, David B.

1987-01-01

Noise data on the Large-scale Advanced Propfan (LAP) propeller model SR-7A were taken in the NASA Lewis Research Center 8 x 6 foot Wind Tunnel. The maximum blade passing tone noise first rises with increasing helical tip Mach number to a peak level, then remains the same or decreases from its peak level when going to higher helical tip Mach numbers. This trend was observed for operation at both constant advance ratio and approximately equal thrust. This noise reduction or, leveling out at high helical tip Mach numbers, points to the use of higher propeller tip speeds as a possible method to limit airplane cabin noise while maintaining high flight speed and efficiency. Projections of the tunnel model data are made to the full scale LAP propeller mounted on the test bed aircraft and compared with predictions. The prediction method is found to be somewhat conservative in that it slightly overpredicts the projected model data at the peak.

Comparison of electron-beam and ungated helical CT in detecting coronary arterial calcification by using a working heart phantom and artificial coronary arteries.

PubMed

Hopper, Kenneth D; Strollo, Diane C; Mauger, David T

2002-02-01

To determine the sensitivity and specificity of cardiac gated electron-beam computed tomography (CT) and ungated helical CT in detecting and quantifying coronary arterial calcification (CAC) by using a working heart phantom and artificial coronary arteries. A working heart phantom simulating normal cardiac motion and providing attenuation equal to that of an adult thorax was used. Thirty tubes with a 3-mm inner diameter were internally coated with pulverized human cortical bone mixed with epoxy glue to simulate minimal (n = 10), mild (n = 10), or severe (n = 10) calcified plaques. Ten additional tubes were not coated and served as normal controls. The tubes were attached to the same location on the phantom heart and scanned with electron-beam CT and helical CT in horizontal and vertical planes. Actual plaque calcium content was subsequently quantified with atopic spectroscopy. Two blinded experienced radiologic imaging teams, one for each CT system, separately measured calcium content in the model vessels by using a Hounsfield unit threshold of 130 or greater. The sensitivity and specificity of electron-beam CT in detecting CAC were 66.1% and 80.0%, respectively. The sensitivity and specificity of helical CT were 96.4% and 95.0%, respectively. Electron-beam CT was less reliable when vessels were oriented vertically (sensitivity and specificity, 71.4% and 70%; 95% CI: 39.0%, 75.0%) versus horizontally (sensitivity and specificity, 60.7% and 90.0%; 95% CI: 48.0%, 82.0%). When a correction factor was applied, the volume of calcified plaque was statistically better quantified with helical CT than with electron-beam CT (P =.004). Ungated helical CT depicts coronary arterial calcium better than does gated electron-beam CT. When appropriate correction factors are applied, helical CT is superior to electron-beam CT in quantifying coronary arterial calcium. Although further work must be done to optimize helical CT grading systems and scanning protocols, the data of this study demonstrated helical CT's inherent advantage over currently commercially available electron-beam CT systems in CAC detection and quantification.

76 FR 57075 - Helical Spring Lock Washers From China and Taiwan

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-15

... INTERNATIONAL TRADE COMMISSION [Investigation Nos. 731-TA-624-625; Third Review] Helical Spring... duty orders on helical spring lock washers from China and Taiwan. AGENCY: United States International...) to determine whether revocation of the antidumping duty orders on helical spring lock washers from...

Effects of Helicity on Lagrangian and Eulerian Time Correlations in Turbulence

NASA Technical Reports Server (NTRS)

Rubinstein, Robert; Zhou, Ye

1998-01-01

Taylor series expansions of turbulent time correlation functions are applied to show that helicity influences Eulerian time correlations more strongly than Lagrangian time correlations: to second order in time, the helicity effect on Lagrangian time correlations vanishes, but the helicity effect on Eulerian time correlations is nonzero. Fourier analysis shows that the helicity effect on Eulerian time correlations is confined to the largest inertial range scales. Some implications for sound radiation by swirling flows are discussed.

Processing and plating helical metallic coils

NASA Technical Reports Server (NTRS)

1972-01-01

The results of research efforts to develop an optimized nickel cobalt coating suitable as a recording medium are outlined. The coating is to be used directly on a BeCu helical coil substrate of a helical coil NASA recorder. Specifically, efforts were made to: optimize the coating thickness; establish processes and techniques adaptable for the production of finalized plated helical coils; design and fabricate the equipment required for production and testing of the coils; and deliver finalized helical coils to NASA.

Hardness and microstructure analysis of damaged gear caused by adhesive wear

NASA Astrophysics Data System (ADS)

Mahendra, Rizky Budi; Nugroho, Sri; Ismail, Rifky

2018-03-01

This study was a result from research on repairing project of damaged elevator gear box. The objective of this research is to analyze the failure part on elevator gearbox at flourmill factory. The equipment was damaged after one year installed and running on factory. Severe wear was occurred on high speed helical gear. These helical gear was one of main part of elevator gearbox in flour mill manufacture. Visually, plastic deformation didn't occurred and not visible on the failure helical gear shaft. Some test would be performed to check the chemical composition, microstructure and hardness of failure helical gear. The material of failure helical gear shaft was a medium carbon steel alloy. The microstructure was showed a martensitic phase formed on the surface to the center area of gear shaft. Otherwise, the depth of hardness layer slight formed on surface and lack depth of hardness layer was a main trigger of severe wear. It was not enough to resist wear due to friction caused by rolling and sliding on surface between high speed gear and low speed gear. Enhancement of hardness layer on surface and depth of hardness layer will make the component has more long life time. Furthermore, to perform next research is needed to analyze the reliability of enhanced hardness on layer and depth of hardness layer on helical gear shaft.

Space confinement and rotation stress induced self-organization of double-helix nanostructure: a nanotube twist with a moving catalyst head.

PubMed

Zhao, Meng-Qiang; Zhang, Qiang; Tian, Gui-Li; Huang, Jia-Qi; Wei, Fei

2012-05-22

Inorganic materials with double-helix structure have attracted intensive attention due to not only their elegant morphology but also their amazing morphology-related potential applications. The investigation on the formation mechanism of the inorganic double-helix nanostructure is the first step for the fundamental studies of their materials or physical properties. Herein, we demonstrated the space confinement and rotation stress induced self-organization mechanism of the carbon nanotube (CNT)-array double helices under scanning electron microscopy by directly observing their formation process from individual layered double hydroxide flakes, which is a kind of hydrotalcite-like material composed of positively charged layers and charge-balancing interlayer anions. Space confinement is considered to be the most important extrinsic factor for the formation of CNT-array double helices. Synchronous growth of the CNT arrays oppositely from LDH flakes with space confinement on both sides at the same time is essential for the growth of CNT-array double helices. Coiling of the as-grown CNT arrays into double helices will proceed by self-organization, tending to the most stable morphology in order to release their internal rotation stress. Based on the demonstrated mechanism, effective routes were carried out to improve the selectivity for CNT-array double helices. The work provides a promising method for the fabrication of double-helix nanostructures with their two helices connected at the end by self-assembly.

Circular dichroism and UV resonance Raman study of the impact of alcohols on the Gibbs free energy landscape of an α-helical peptide†

PubMed Central

Xiong, Kan; Asher, Sanford A

2010-01-01

We used CD and UV resonance Raman spectroscopy to study the impact of alcohols on the conformational equilibria and relative Gibbs free energy landscapes along the Ramanchandran Ψ-coordinate of a mainly poly-ala peptide, AP of sequence AAAAA(AAARA)3A. 2,2,2-trifluroethanol (TFE) most stabilizes the α-helical-like conformations, followed by ethanol, methanol and pure water. The π-bulge conformation is stabilized more than the α-helix, while the 310-helix is destabilized due to the alcohol increased hydrophobicity. Turns are also stabilized by alcohols. We also found that while TFE induces more α-helices, it favors multiple, shorter helix segments. PMID:20225890

Data on diverse roles of helix perturbations in membrane proteins.

PubMed

Shelar, Ashish; Bansal, Manju

2016-12-01

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

Conversion from mutual helicity to self-helicity observed with IRIS

NASA Astrophysics Data System (ADS)

Li, L. P.; Peter, H.; Chen, F.; Zhang, J.

2014-10-01

Context. In the upper atmosphere of the Sun observations show convincing evidence for crossing and twisted structures, which are interpreted as mutual helicity and self-helicity. Aims: We use observations with the new Interface Region Imaging Spectrograph (IRIS) to show the conversion of mutual helicity into self-helicity in coronal structures on the Sun. Methods: Using far UV spectra and slit-jaw images from IRIS and coronal images and magnetograms from SDO, we investigated the evolution of two crossing loops in an active region, in particular, the properties of the Si IV line profile in cool loops. Results: In the early stage two cool loops cross each other and accordingly have mutual helicity. The Doppler shifts in the loops indicate that they wind around each other. As a consequence, near the crossing point of the loops (interchange) reconnection sets in, which heats the plasma. This is consistent with the observed increase of the line width and of the appearance of the loops at higher temperatures. After this interaction, the two new loops run in parallel, and in one of them shows a clear spectral tilt of the Si IV line profile. This is indicative of a helical (twisting) motion, which is the same as to say that the loop has self-helicity. Conclusions: The high spatial and spectral resolution of IRIS allowed us to see the conversion of mutual helicity to self-helicity in the (interchange) reconnection of two loops. This is observational evidence for earlier theoretical speculations. Movie associated with Fig. 1 and Appendix A are available in electronic form at http://www.aanda.org

Comparative NMR Analysis of an 80-Residue G Protein-Coupled Receptor Fragment in Two Membrane Mimetic Environments

PubMed Central

LS, Cohen; B, Arshava; A, Neumoin; JM, Becker; P, Güntert; O, Zerbe; Naider, F

2011-01-01

Fragments of integral membrane proteins have been used to study the physical chemical properties of regions of transporters and receptors. Ste2p(G31-T110) is an 80-residue polypeptide which contains a portion of the N-terminal domain, transmembrane domain 1 (TM1), intracellular loop 1, TM2 and part of extracellular loop 2 of the α-factor receptor (Ste2p) from Saccharomyces cerevisiae. The structure of this peptide was previously determined to form a helical hairpin in lyso-palmitoylphosphatidyl-glycerol micelles (LPPG)[1]. Herein, we perform a systematic comparison of the structure of this protein fragment in micelles and trifluoroethanol(TFE):water in order to understand whether spectra recorded in organic:aqueous medium can facilitate the structure determination in a micellar environment. Using uniformly labeled peptide and peptide selectively protonated on Ile, Val and Leu methyl groups in a perdeuterated background and a broad set of 3D NMR experiments we assigned 89% of the observable atoms. NOEs and chemical shift analysis were used to define the helical regions of the fragment. Together with constraints from paramagnetic spin labeling, NOEs were used to calculate a transiently folded helical hairpin structure for this peptide in TFE:water. Correlation of chemical shifts was insufficient to transfer assignments from TFE:water to LPPG spectra in the absence of further information. PMID:21791199

Magnetohydrodynamic Models of Molecular Tornadoes

NASA Astrophysics Data System (ADS)

Au, Kelvin; Fiege, Jason D.

2017-07-01

Recent observations near the Galactic Center (GC) have found several molecular filaments displaying striking helically wound morphology that are collectively known as molecular tornadoes. We investigate the equilibrium structure of these molecular tornadoes by formulating a magnetohydrodynamic model of a rotating, helically magnetized filament. A special analytical solution is derived where centrifugal forces balance exactly with toroidal magnetic stress. From the physics of torsional Alfvén waves we derive a constraint that links the toroidal flux-to-mass ratio and the pitch angle of the helical field to the rotation laws, which we find to be an important component in describing the molecular tornado structure. The models are compared to the Ostriker solution for isothermal, nonmagnetic, nonrotating filaments. We find that neither the analytic model nor the Alfvén wave model suffer from the unphysical density inversions noted by other authors. A Monte Carlo exploration of our parameter space is constrained by observational measurements of the Pigtail Molecular Cloud, the Double Helix Nebula, and the GC Molecular Tornado. Observable properties such as the velocity dispersion, filament radius, linear mass, and surface pressure can be used to derive three dimensionless constraints for our dimensionless models of these three objects. A virial analysis of these constrained models is studied for these three molecular tornadoes. We find that self-gravity is relatively unimportant, whereas magnetic fields and external pressure play a dominant role in the confinement and equilibrium radial structure of these objects.

Ion Heating During Local Helicity Injection Plasma Startup in the Pegasus ST

NASA Astrophysics Data System (ADS)

Burke, M. G.; Barr, J. L.; Bongard, M. W.; Fonck, R. J.; Hinson, E. T.; Perry, J. M.; Reusch, J. A.

2015-11-01

Plasmas in the Pegasus ST are initiated either through standard, MHD stable, inductive current drive or non-solenoidal local helicity injection (LHI) current drive with strong reconnection activity, providing a rich environment to study ion dynamics. During LHI discharges, a large amount of impurity ion heating has been observed, with the passively measured impurity Ti as high as 800 eV compared to Ti ~ 60 eV and Te ~ 175 eV during standard inductive current drive discharges. In addition, non-thermal ion velocity distributions are observed and appear to be strongest near the helicity injectors. The ion heating is hypothesized to be a result of large-scale magnetic reconnection activity, as the amount of heating scales with increasing fluctuation amplitude of the dominant, edge localized, n =1 MHD mode. An approximate temporal scaling of the heating with the amplitude of higher frequency magnetic fluctuations has also been observed, with large amounts of power spectral density present at several impurity ion cyclotron frequencies. Recent experiments have focused on investigating the impurity ion heating scaling with the ion charge to mass ratio as well as the reconnecting field strength. The ion charge to mass ratio was modified by observing different impurity charge states in similar LHI plasmas while the reconnecting field strength was modified by changing the amount of injected edge current. Work supported by US DOE grant DE-FG02-96ER54375.

3D magnetic field configuration of small-scale reconnection events in the solar plasma atmosphere

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

Shimizu, T., E-mail: shimizu@solar.isas.jaxa.jp; Department of Earth and Planetary Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033

2015-10-15

The outer solar atmosphere, i.e., the corona and the chromosphere, is replete with small energy-release events, which are accompanied by transient brightening and jet-like ejections. These events are considered to be magnetic reconnection events in the solar plasma, and their dynamics have been studied using recent advanced observations from the Hinode spacecraft and other observatories in space and on the ground. These events occur at different locations in the solar atmosphere and vary in their morphology and amount of the released energy. The magnetic field configurations of these reconnection events are inferred based on observations of magnetic fields at themore » photospheric level. Observations suggest that these magnetic configurations can be classified into two groups. In the first group, two anti-parallel magnetic fields reconnect to each other, yielding a 2D emerging flux configuration. In the second group, helical or twisted magnetic flux tubes are parallel or at a relative angle to each other. Reconnection can occur only between anti-parallel components of the magnetic flux tubes and may be referred to as component reconnection. The latter configuration type may be more important for the larger class of small-scale reconnection events. The two types of magnetic configurations can be compared to counter-helicity and co-helicity configurations, respectively, in laboratory plasma collision experiments.« less

Finite size effect on hydrogen bond cooperativity in (Ala)n polypeptides: A DFT study using numeric atom-centered orbitals

NASA Astrophysics Data System (ADS)

Blum, Volker; Ireta, Joel; Scheffler, Matthias

2007-03-01

An accurate representation of the energetic contribution Ehb of hydrogen bonds to structure formation is paramount to understand the secondary structure stability of proteins, both qualitatively and quantitatively. However, Ehb depends strongly on its environment, and even on the surrounding peptide conformation itself. For instance, a short α-helical polypeptide (Ala)4 can not be stabilized by its single hydrogen bond, whereas an infinite α-helical chain (Ala)∞ is clearly energetically stable over a fully extended conformation. We here use all-electron density functional calculations in the PBE generalized gradient approximation by a recently developed, computationally efficient numeric atom-centered orbital based code^1 to investigate this H-bond cooperativity that is intrinsic to Alanine-based polypeptides (Ala)n (n=1-20,∞). We compare finite and infinite prototypical helical conformations (α, π, 310) on equal footing, with both neutral and ionic termination for finite (Ala)n peptides. Moderately sized NAO basis sets allow to capture Ehb with meV accuracy, revealing a clear jump in Ehb (cooperativity) when two H-bonds first appear in line, followed by slower and more continuous increase of Ehb towards n->∞. ^1 V. Blum, R. Gehrke, P. Havu, V. Havu, M. Scheffler, The FHI Ab Initio Molecular Simulations (aims) Project, Fritz-Haber-Institut, Berlin (2006).

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

Spin-lattice-coupling-mediated magnetoferroelectric phase transition induced by uniaxial pressure in multiferroic CuFe1 -xMxO2 (M =Ga , Al)

NASA Astrophysics Data System (ADS)

Tamatsukuri, Hiromu; Mitsuda, Setsuo; Nakamura, Tenfu; Takata, Kouhei; Nakajima, Taro; Prokes, Karel; Yokaichiya, Fabiano; Kiefer, Klaus

2017-05-01

We have investigated magnetic and ferroelectric (dielectric) properties of multiferroic CuFe0.982Ga0.018O2 , CuFe0.965Ga0.035O2 , and CuFe0.95Al0.05O2 under applied uniaxial pressure p up to 600 MPa. Unlike the results of the almost same experiments on CuFeO2 [Tamatsukuri et al., Phys. Rev. B 94, 174402 (2016), 10.1103/PhysRevB.94.174402], we have found that the application of p induces a new ferroelectric phase, which is different from the well-studied spin-driven ferroelectric phase with helical magnetic ordering, in all the doped samples investigated here. We have also constructed the temperature versus p magnetoelectric phase diagrams of the three samples. The ferroelectric polarization in the p -induced ferroelectric phase lies along the [110] direction as in the helical magnetoferroelectric phase, and its value is comparable with or larger than that in the helical magnetoferroelectric phase. The magnetic structure in the p -induced ferroelectric phase seems to be of a collinear sinusoidal type. Although this magnetic structure itself does not break the inversion symmetry, it is considered to play an important role in the origin of ferroelectricity in the p -induced ferroelectric phase through the spin-lattice coupling in this system.

Polarization-dependent plasmonic photocurrents in two-dimensional electron systems

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

Popov, V. V., E-mail: popov-slava@yahoo.co.uk; Saratov State University, Saratov 410012; Saratov Scientific Center of the Russian Academy of Sciences, Saratov 410028

2016-06-27

Plasmonic polarization dependent photocurrents in a homogeneous two-dimensional electron system are studied. Those effects are completely different from the photon drag and electronic photogalvanic effects as well as from the plasmonic ratchet effect in a density modulated two-dimensional electron system. Linear and helicity-dependent contributions to the photocurrent are found. The linear contribution can be interpreted as caused by the longitudinal and transverse plasmon drag effect. The helicity-dependent contribution originates from the non-linear electron convection and changes its sign with reversing the plasmonic field helicity. It is shown that the helicity-dependent component of the photocurrent can exceed the linear one bymore » several orders of magnitude in high-mobility two-dimensional electron systems. The results open possibilities for all-electronic detection of the radiation polarization states by exciting the plasmonic photocurrents in two-dimensional electron systems.« less

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.

Structural mechanics and helical geometry of thin elastic composites.

PubMed

Wada, Hirofumi

2016-09-21

Helices are ubiquitous in nature, and helical shape transition is often observed in residually stressed bodies, such as composites, wherein materials with different mechanical properties are glued firmly together to form a whole body. Inspired by a variety of biological examples, the basic physical mechanism responsible for the emergence of twisting and bending in such thin composite structures has been extensively studied. Here, we propose a simplified analytical model wherein a slender membrane tube undergoes a helical transition driven by the contraction of an elastic ribbon bound to the membrane surface. We analytically predict the curvature and twist of an emergent helix as functions of differential strains and elastic moduli, which are confirmed by our numerical simulations. Our results may help understand shapes observed in different biological systems, such as spiral bacteria, and could be applied to novel designs of soft machines and robots.

Combined process "helical rolling-pressing" and its effect on the microstructure of ferrous and non-ferrous materials

NASA Astrophysics Data System (ADS)

Naizabekov, Abdrakhman; Lezhnev, Sergey; Arbuz, Alexandr; Panin, Evgeniy

2018-02-01

Ultrafine-grained materials are one of the most promising structural and functional materials. However, the known methods of obtaining them are not enough powerful and technologically advanced for profitable industrial applications. Development of the combined process "helical rolling-pressing" is an attempt to bring technology to produce ultrafine-grained materials to the industry. The combination of intense processing of the surface by helical rolling and the entire cross section of workpiece in equal channel angular matrix, with intense deformation by torsion between rolls and matrix will increase the degree of deformation per pass and allows to mutually compensate disadvantages of these methods in the case of their separate use. This paper describes the development of a laboratory stand and study of influence of combined process "helical rolling-pressing"on the microstructure of tool steel, technical copper and high alloy stainless high-temperature steel.

Anomalous transport and generalized axial charge

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

Kirilin, Vladimir P.; Sadofyev, Andrey V.

For this article, we continue studying the modification of the axial charge in chiral media by macroscopic helicities. Recently it was shown that magnetic reconnections result in a persistent current of zero mode along flux tubes. Here we argue that in general a change in the helical part of the generalized axial charge results in the same phenomenon. Thus one may say that there is a novel realization of chiral effects requiring no initial chiral asymmetry. The transfer of flow helicity to zero modes is analyzed in a toy model based on a vortex reconnection in a chiral superfluid. Then,more » we discuss the balance between the two competing processes effect of reconnections and the chiral instability on the example of magnetic helicity. We argue that in the general case there is a possibility for the distribution of the axial charge between the magnetic and fermionic forms at the end of the instability.« less

Paired Helical Filaments of Inclusion-Body Myositis Muscle Contain RNA and Survival Motor Neuron Protein

PubMed Central

Broccolini, Aldobrando; Engel, W. King; Alvarez, Renate B.; Askanas, Valerie

2000-01-01

Sporadic inclusion-body myositis (s-IBM) is the most common progressive muscle disease of older persons. Pathologically, the muscle biopsy manifests various degrees of inflammation and specific vacuolar degeneration of muscle fibers characterized by paired helical filaments (PHFs) composed of phosphorylated tau. IBM vacuolated fibers also contain accumulations of several other Alzheimer-characteristic proteins. Molecular mechanisms leading to formation of the PHFs and accumulations of proteins in IBM muscle are not known. We report that the abnormal muscle fibers of IBM contained (i) acridine-orange-positive RNA inclusions that colocalized with the immunoreactivity of phosphorylated tau and (ii) survival motor neuron protein immunoreactive inclusions, which by immuno-electron microscopy were confined to paired helical filaments. This study demonstrates two novel components of the IBM paired helical filaments, which may lead to better understanding of their pathogenesis. PMID:10751338

Manipulation of wavefront using helical metamaterials.

PubMed

Yang, Zhenyu; Wang, Zhaokun; Tao, Huan; Zhao, Ming

2016-08-08

Helical metamaterials, a kind of 3-dimensional structure, has relatively strong coupling effect among the helical nano-wires. Therefore, it is expected to be a good candidate for generating phase shift and controlling wavefront with high efficiency. In this paper, using the finite-difference time-domain (FDTD) method, we studied the phase shift properties in the helical metamaterials. It is found that the phase shift occurs for both transmitted and reflected light waves. And the maximum of reflection coefficients can reach over 60%. In addition, the phase shift (φ) is dispersionless in the range of 600 nm to 860 nm, that is, it is only dominated by the initial angle (θ) of the helix. The relationship between them is φ = ± 2θ. Using Jones calculus we give a further explanation for these properties. Finally, by arranging the helixes in an array with a constant phase gradient, the phenomenon of anomalous refraction was also observed in a broad wavelength range.

Anomalous transport and generalized axial charge

DOE PAGES

Kirilin, Vladimir P.; Sadofyev, Andrey V.

2017-07-25

For this article, we continue studying the modification of the axial charge in chiral media by macroscopic helicities. Recently it was shown that magnetic reconnections result in a persistent current of zero mode along flux tubes. Here we argue that in general a change in the helical part of the generalized axial charge results in the same phenomenon. Thus one may say that there is a novel realization of chiral effects requiring no initial chiral asymmetry. The transfer of flow helicity to zero modes is analyzed in a toy model based on a vortex reconnection in a chiral superfluid. Then,more » we discuss the balance between the two competing processes effect of reconnections and the chiral instability on the example of magnetic helicity. We argue that in the general case there is a possibility for the distribution of the axial charge between the magnetic and fermionic forms at the end of the instability.« less

Geometric scalings for the electrostatically driven helical plasma state

NASA Astrophysics Data System (ADS)

Akçay, Cihan; Finn, John M.; Nebel, Richard A.; Barnes, Daniel C.

2017-12-01

A new plasma state has been investigated [Akcay et al., Phys. Plasmas 24, 052503 (2017)], with a uniform applied axial magnetic field in a periodic cylinder of length L = 2 π R , driven by helical electrodes. The drive is single helicity, depending on m θ + k z = m θ - n ζ , where ζ = z / R and k = - n / R . For strong ( m , n ) = ( 1 , 1 ) drive, the state was found to have a strong axial mean current density, with a mean-field safety factor q 0 ( r ) just above the pitch of the electrodes m / n = 1 in the interior. This state has possible applications to DC electrical transformers and tailoring of the current profile in tokamaks. We study two geometric issues of interest for these applications: (i) scaling of properties with the plasma length or aspect ratio and (ii) behavior for different helicities, specifically ( m , n ) = ( 1 , n ) for n > 1 and ( m , n ) = ( 2 , 1 ) .

Electrochemical sensor for rutin detection based on Au nanoparticle-loaded helical carbon nanotubes

NASA Astrophysics Data System (ADS)

Yang, Haitang; Li, Bingyue; Cui, Rongjing; Xing, Ruimin; Liu, Shanhu

2017-10-01

The key step in the fabrication of highly active electrochemical sensors is seeking multifunctional nanocomposites as electrode modified materials. In this study, the gold nanoparticle-decorated helical carbon nanotube nanocomposites (AuNPs-HCNTs) were fabricated for rutin detection because of its superior sensitivity, the chemical stability of AuNPs, and the superior conductivity and unique 3D-helical structure of helical carbon nanotubes. Results showed the prepared nanocomposites exhibited superior electrocatalytic activity towards rutin due to the synergetic effects of AuNPs and HCNTs. Under the optimized conditions, the developed sensor exhibited a linear response range from 0.1 to 31 μmol/L for rutin with a low detectable limit of 81 nmol/L. The proposed method might offer a possibility for electrochemical analysis of rutin in Chinese medical analysis or serum monitoring owing to its low cost, simplicity, high sensitivity, good stability, and few interferences against common coexisting ions in real samples.

Improved circumferential shaft seal

NASA Technical Reports Server (NTRS)

Ludwig, L. P.; Strom, T. N.

1974-01-01

Comparative tests of modified and unmodified carbon ring seals showed that addition of helical grooves to conventional segmented carbon ring seals reduced leakage significantly. Modified seal was insensitive to shaft runout and to flooding by lubricant.

Heat Transfer Measurements of Internally Finned Rotating Heat Pipes.

DTIC Science & Technology

1983-12-01

42 C. RESULTS OF STRAIGHT 22 FIN CONDENSER o . o . 51 D. RESULTS OF HELICAL 14 AND 16 FIN CONDENSER o 51 E. RESULTS OF HELICAL 36 FIN...88 C.6 RESULTS OF STRAIGHT 22 FIN CONDENSER AT 2800 RPM . . . . . . . . . . . . . . . . . . . . 89 C.7 RESULTS OF HELICAL 16 FIN CONDENSER ...AT 700 RPM . 90 C.8 RESULTS OF HELICAL 16 PIN CONDENSER AT 1600 RPM . 91 C.9 RESULTS OF HELICAL 16 PIN CONDENSER AT 2800 RPM . 92 C. 10 RESULTS OF

Helical patterns of magnetization and magnetic charge density in iron whiskers

NASA Astrophysics Data System (ADS)

Templeton, Terry L.; Hanham, Scott D.; Arrott, Anthony S.

2018-05-01

Studies with the (1 1 1) axis along the long axis of an iron whisker, 40 years ago, showed two phenomena that have remained unexplained: 1) In low fields, there are six peaks in the ac susceptibility, separated by 0.2 mT; 2) Bitter patterns showed striped domain patterns. Multipole columns of magnetic charge density distort to form helical patterns of the magnetization, accounting for the peaks in the susceptibility from the propagation of edge solitons along the intersections of the six sides of a (1 1 1) whisker. The stripes follow the helices. We report micromagnetic simulations in cylinders with various geometries for the cross-sections from rectangular, to hexagonal, to circular, with wide ranges of sizes and lengths, and different anisotropies, including (0 0 1) whiskers and the hypothetical case of no anisotropy. The helical patterns have been there in previous studies, but overlooked. The surface swirls and body helices are connected, but have their own individual behaviors. The magnetization patterns are more easily understood when viewed observing the scalar divergences of the magnetization as isosurfaces of magnetic charge density. The plus and minus charge densities form columns that interact with unlike charges attracting, but not annihilating as they are paid for by a decrease in exchange energy. Just as they start to form the helix, the columns are multipoles. If one could stretch the columns, the self-energy of the charges in a column would be diminished while making the attractive interactions of the unlike charges larger. The columns elongate by becoming helical. The visualization of 3-D magnetic charge distributions aids in the understanding of magnetization in soft magnetic materials.

Reversed Field Pinch helical self-organization studies with the volume preserving field line tracing code NEMATO

NASA Astrophysics Data System (ADS)

Bonfiglio, D.; Veranda, M.; Cappello, S.; Chacon, L.; Escande, D. F.; Piovesan, P.

2009-11-01

The existence of a Reversed Field Pinch (RFP) dynamo as a (laminar) helical self-organization was anticipated by MHD numerical studies [1]. High current operation in RFX-mod experiment shows such a helical self-organization: strong internal electron transport barriers (ITB) appear and magnetic chaos healing is diagnosed when Single Helical Axis (SHAx) regimes are achieved [2]. We present results of the field line tracing code NEMATO [3] applied to study the magnetic topology resulting from 3D MHD simulations, with the aim of clarifying the conditions for chaos healing in SHAx states. First tests confirm the basic picture: the magnetic chaos due to island overlap is significantly reduced after the expulsion of the dominant mode separatrix. The possible synergy with the presence of magnetic and/or flow shear at the SHAx ITB will also be discussed [4].[4pt] [1] S. Cappello, Plasma Phys. Control. Fusion (2004) & references therein [0pt] [2] R. Lorenzini et al., Nature Phys. (2009) [0pt] [3] J. M. Finn and L. Chacon, Phys. Plasmas (2005) [0pt] [4] M.E. Puiatti et al invited presentation EPS 2009 conference, submitted to Plasma Phys. Control. Fusion

Sterilization of single-use helical stone baskets: an experimental study.

PubMed

Korkes, Fernando; Menezes, Alex; Silva, Cely Barreto da; Fernandes, Roni de Carvalho; Perez, Marjo Deninson Cardenuto

2011-03-01

To experimentally evaluate the efficacy of a standard sterilization protocol employed during reuse of disposable helical stone baskets. Study performed on 20 helical stone baskets: 10 were used in the initial validation process, contaminated with Escherichia coli ATCC 25922 and imprinted on Müeller-Hinton media; 10 catheters were contaminated with Geobacillus stearothermophilus ATCC 7953, processed, inoculated in TSB and incubated in a water bath at a temperature of 55°C. Bacterial growth was evaluated after 1, 3, 5 and 7 days. After sterilization, stone baskets were also opened and closed 40 times to check for functional problems. All plastic and basket parts were carefully checked for damages. After the 72-hour incubation period, there was growth of E. coli ATCC 25922 in 100% of imprints. After the sterilization process and up to 7 days incubation period on a blood agar plate, there was no growth of G. stearothermophilus ATCC 7953 or any other bacteria. There were no functional problems or damage to baskets after the sterilization process. The ethylene oxide system is efficacious and safe for sterilization of disposable helical stone baskets. However, further clinical studies are required and should provide more safety information.

Approaches to ab initio molecular replacement of α-helical transmembrane proteins.

PubMed

Thomas, Jens M H; Simkovic, Felix; Keegan, Ronan; Mayans, Olga; Zhang, Chengxin; Zhang, Yang; Rigden, Daniel J

2017-12-01

α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.

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.

Competition between B-Z and B-L transitions in a single DNA molecule: Computational studies

NASA Astrophysics Data System (ADS)

Kwon, Ah-Young; Nam, Gi-Moon; Johner, Albert; Kim, Seyong; Hong, Seok-Cheol; Lee, Nam-Kyung

2016-02-01

Under negative torsion, DNA adopts left-handed helical forms, such as Z-DNA and L-DNA. Using the random copolymer model developed for a wormlike chain, we represent a single DNA molecule with structural heterogeneity as a helical chain consisting of monomers which can be characterized by different helical senses and pitches. By Monte Carlo simulation, where we take into account bending and twist fluctuations explicitly, we study sequence dependence of B-Z transitions under torsional stress and tension focusing on the interaction with B-L transitions. We consider core sequences, (GC) n repeats or (TG) n repeats, which can interconvert between the right-handed B form and the left-handed Z form, imbedded in a random sequence, which can convert to left-handed L form with different (tension dependent) helical pitch. We show that Z-DNA formation from the (GC) n sequence is always supported by unwinding torsional stress but Z-DNA formation from the (TG) n sequence, which are more costly to convert but numerous, can be strongly influenced by the quenched disorder in the surrounding random sequence.

Twisted ribbon structure of paired helical filaments revealed by atomic force microscopy.

PubMed Central

Pollanen, M. S.; Markiewicz, P.; Bergeron, C.; Goh, M. C.

1994-01-01

Progressive deposition of phosphorylated tau into the paired helical filaments (PHF) that compose neurofibrillary tangles, dystrophic neurites, and neuropil threads is an obligate feature of Alzheimer's disease. The standard model of PHF structure, derived from electron microscopic studies, suggests that two 8- to 10-nm filaments each composed of three to four protofilaments are wound into a helix with a maximal diameter of -20 nm and a half period of 65 to 80 nm. However, recent vertical platinum-carbon replicas of PHF more closely resemble a thin helical ribbon without constitutive protofilaments. Here we report that native PHF imaged with an atomic force microscope appear as twisted ribbons rather than the generally accepted structure derived from electron microscopic studies. These data imply that the assembly of PHF is not due to the twisting of pair-wise filaments but rather the helical winding of self-associated tau molecules arranged into a flattened structure. Future structural models of PHF should be based on quantitative data obtained from imaging techniques, such as scanning probe microscopy, which do not require harsh specimen preparation procedures. Images Figure 1 PMID:8178938

Twisted ribbon structure of paired helical filaments revealed by atomic force microscopy.

PubMed

Pollanen, M S; Markiewicz, P; Bergeron, C; Goh, M C

1994-05-01

Progressive deposition of phosphorylated tau into the paired helical filaments (PHF) that compose neurofibrillary tangles, dystrophic neurites, and neuropil threads is an obligate feature of Alzheimer's disease. The standard model of PHF structure, derived from electron microscopic studies, suggests that two 8- to 10-nm filaments each composed of three to four protofilaments are wound into a helix with a maximal diameter of -20 nm and a half period of 65 to 80 nm. However, recent vertical platinum-carbon replicas of PHF more closely resemble a thin helical ribbon without constitutive protofilaments. Here we report that native PHF imaged with an atomic force microscope appear as twisted ribbons rather than the generally accepted structure derived from electron microscopic studies. These data imply that the assembly of PHF is not due to the twisting of pair-wise filaments but rather the helical winding of self-associated tau molecules arranged into a flattened structure. Future structural models of PHF should be based on quantitative data obtained from imaging techniques, such as scanning probe microscopy, which do not require harsh specimen preparation procedures.

Is the Lecompte technique the last word on transposition of the great arteries repair for all patients? A magnetic resonance imaging study including a spiral technique two decades postoperatively.

PubMed

Rickers, Carsten; Kheradvar, Arash; Sievers, Hans-Hinrich; Falahatpisheh, Ahmad; Wegner, Philip; Gabbert, Dominik; Jerosch-Herold, Michael; Hart, Chris; Voges, Inga; Putman, Léon M; Kristo, Ines; Fischer, Gunther; Scheewe, Jens; Kramer, Hans-Heiner

2016-06-01

To compare the Lecompte technique and the spiral anastomosis (complete anatomic correction) two decades after arterial switch operation (ASO). Nine patients after primary ASO with Lecompte and 6 selected patients after spiral anastomosis were evaluated 20.8 ± 2.1 years after ASO versus matched controls. Blood flow dynamics and flow profiles (e.g. vorticity, helicity) in the great arteries were quantified from time-resolved 3D magnetic resonance imaging (MRI) phase contrast flow measurements (4D flow MR) in addition to a comprehensive anatomical and functional cardiovascular MRI analysis. Compared with spiral reconstruction, patients with Lecompte showed more vortex formation, supranatural helical blood flow (relative helicity in aorta: 0.036 vs 0.089; P < 0.01), a reduced indexed cross-sectional area of the left pulmonary artery (155 vs 85 mm²/m²; P < 0.001) and more semilunar valve dysfunctions (n = 5 vs 1). There was no difference in elastic aortic wall properties, ventricular function, myocardial perfusion and myocardial fibrosis between the two groups. Cross-sectional area of the aortic sinus was larger in patients than in controls (669 vs 411 mm²/m²; P < 0.01). In the spiral group, the pulmonary root was rotated after ASO more towards the normal left position (P < 0.01). In this study, selected patients with spiral anastomoses showed, two decades after ASO, better physiologically adapted blood flow dynamics, and attained a closer to normal anatomical position of their great arteries, as well as less valve dysfunction. Considering the limitations related to the small number of patients and the novel MRI imaging techniques, these data may provoke reconsidering the optimal surgical approaches to transposition of the great arteries repair. © The Author 2016. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

Real-space processing of helical filaments in SPARX

PubMed Central

Behrmann, Elmar; Tao, Guozhi; Stokes, David L.; Egelman, Edward H.; Raunser, Stefan; Penczek, Pawel A.

2012-01-01

We present a major revision of the iterative helical real-space refinement (IHRSR) procedure and its implementation in the SPARX single particle image processing environment. We built on over a decade of experience with IHRSR helical structure determination and we took advantage of the flexible SPARX infrastructure to arrive at an implementation that offers ease of use, flexibility in designing helical structure determination strategy, and high computational efficiency. We introduced the 3D projection matching code which now is able to work with non-cubic volumes, the geometry better suited for long helical filaments, we enhanced procedures for establishing helical symmetry parameters, and we parallelized the code using distributed memory paradigm. Additional feature includes a graphical user interface that facilitates entering and editing of parameters controlling the structure determination strategy of the program. In addition, we present a novel approach to detect and evaluate structural heterogeneity due to conformer mixtures that takes advantage of helical structure redundancy. PMID:22248449

On the Mysterious Propulsion of Synechococcus

PubMed Central

Ehlers, Kurt; Oster, George

2012-01-01

We propose a model for the self-propulsion of the marine bacterium Synechococcus utilizing a continuous looped helical track analogous to that found in Myxobacteria [1]. In our model cargo-carrying protein motors, driven by proton-motive force, move along a continuous looped helical track. The movement of the cargo creates surface distortions in the form of small amplitude traveling ridges along the S-layer above the helical track. The resulting fluid motion adjacent to the helical ribbon provides the propulsive thrust. A variation on the helical rotor model of [1] allows the motors to be anchored to the peptidoglycan layer, where they drive rotation of the track creating traveling helical waves along the S-layer. We derive expressions relating the swimming speed to the amplitude, wavelength, and velocity of the surface waves induced by the helical rotor, and show that they fall in reasonable ranges to explain the velocity and rotation rate of swimming Synechococcus. PMID:22567124

γ5 in the four-dimensional helicity scheme

NASA Astrophysics Data System (ADS)

Gnendiger, C.; Signer, A.

2018-05-01

We investigate the regularization-scheme dependent treatment of γ5 in the framework of dimensional regularization, mainly focusing on the four-dimensional helicity scheme (fdh). Evaluating distinctive examples, we find that for one-loop calculations, the recently proposed four-dimensional formulation (fdf) of the fdh scheme constitutes a viable and efficient alternative compared to more traditional approaches. In addition, we extend the considerations to the two-loop level and compute the pseudoscalar form factors of quarks and gluons in fdh. We provide the necessary operator renormalization and discuss at a practical level how the complexity of intermediate calculational steps can be reduced in an efficient way.

Mediastinal irradiation in a patient affected by lung carcinoma after heart transplantation: Helical tomotherapy versus three dimensional conformal radiotherapy.

PubMed

Giugliano, Francesca M; Iorio, Vincenzo; Cammarota, Fabrizio; Toledo, Diego; Senese, Rossana; Francomacaro, Ferdinando; Muto, Matteo; Muto, Paolo

2016-04-26

Patients who have undergone solid organ transplants are known to have an increased risk of neoplasia compared with the general population. We report our experience using mediastinal irradiation with helical tomotherapy versus three-dimensional conformal radiation therapy to treat a patient with lung carcinoma 15 years after heart transplantation. Our dosimetric evaluation showed no particular difference between the techniques, with the exception of some organs. Mediastinal irradiation after heart transplantation is feasible and should be considered after evaluation of the risk. Conformal radiotherapy or intensity-modulated radiotherapy appears to be the appropriate treatment in heart-transplanted oncologic patients.

Parametric tests of a traction drive retrofitted to an automotive gas turbine

NASA Technical Reports Server (NTRS)

Rohn, D. A.; Lowenthal, S. H.; Anderson, N. E.

1980-01-01

The results of a test program to retrofit a high performance fixed ratio Nasvytis Multiroller Traction Drive in place of a helical gear set to a gas turbine engine are presented. Parametric tests up to a maximum engine power turbine speed of 45,500 rpm and to a power level of 11 kW were conducted. Comparisons were made to similar drives that were parametrically tested on a back-to-back test stand. The drive showed good compatibility with the gas turbine engine. Specific fuel consumption of the engine with the traction drive speed reducer installed was comparable to the original helical gearset equipped engine.

Sinogram restoration in computed tomography with an edge-preserving penalty

PubMed Central

Little, Kevin J.; La Rivière, Patrick J.

2015-01-01

Purpose: With the goal of producing a less computationally intensive alternative to fully iterative penalized-likelihood image reconstruction, our group has explored the use of penalized-likelihood sinogram restoration for transmission tomography. Previously, we have exclusively used a quadratic penalty in our restoration objective function. However, a quadratic penalty does not excel at preserving edges while reducing noise. Here, we derive a restoration update equation for nonquadratic penalties. Additionally, we perform a feasibility study to extend our sinogram restoration method to a helical cone-beam geometry and clinical data. Methods: A restoration update equation for nonquadratic penalties is derived using separable parabolic surrogates (SPS). A method for calculating sinogram degradation coefficients for a helical cone-beam geometry is proposed. Using simulated data, sinogram restorations are performed using both a quadratic penalty and the edge-preserving Huber penalty. After sinogram restoration, Fourier-based analytical methods are used to obtain reconstructions, and resolution-noise trade-offs are investigated. For the fan-beam geometry, a comparison is made to image-domain SPS reconstruction using the Huber penalty. The effects of varying object size and contrast are also investigated. For the helical cone-beam geometry, we investigate the effect of helical pitch (axial movement/rotation). Huber-penalty sinogram restoration is performed on 3D clinical data, and the reconstructed images are compared to those generated with no restoration. Results: We find that by applying the edge-preserving Huber penalty to our sinogram restoration methods, the reconstructed image has a better resolution-noise relationship than an image produced using a quadratic penalty in the sinogram restoration. However, we find that this relatively straightforward approach to edge preservation in the sinogram domain is affected by the physical size of imaged objects in addition to the contrast across the edge. This presents some disadvantages of this method relative to image-domain edge-preserving methods, although the computational burden of the sinogram-domain approach is much lower. For a helical cone-beam geometry, we found applying sinogram restoration in 3D was reasonable and that pitch did not make a significant difference in the general effect of sinogram restoration. The application of Huber-penalty sinogram restoration to clinical data resulted in a reconstruction with less noise while retaining resolution. Conclusions: Sinogram restoration with the Huber penalty is able to provide better resolution-noise performance than restoration with a quadratic penalty. Additionally, sinogram restoration with the Huber penalty is feasible for helical cone-beam CT and can be applied to clinical data. PMID:25735286

Sinogram restoration in computed tomography with an edge-preserving penalty

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

Little, Kevin J., E-mail: little@uchicago.edu; La Rivière, Patrick J.

2015-03-15

Purpose: With the goal of producing a less computationally intensive alternative to fully iterative penalized-likelihood image reconstruction, our group has explored the use of penalized-likelihood sinogram restoration for transmission tomography. Previously, we have exclusively used a quadratic penalty in our restoration objective function. However, a quadratic penalty does not excel at preserving edges while reducing noise. Here, we derive a restoration update equation for nonquadratic penalties. Additionally, we perform a feasibility study to extend our sinogram restoration method to a helical cone-beam geometry and clinical data. Methods: A restoration update equation for nonquadratic penalties is derived using separable parabolic surrogatesmore » (SPS). A method for calculating sinogram degradation coefficients for a helical cone-beam geometry is proposed. Using simulated data, sinogram restorations are performed using both a quadratic penalty and the edge-preserving Huber penalty. After sinogram restoration, Fourier-based analytical methods are used to obtain reconstructions, and resolution-noise trade-offs are investigated. For the fan-beam geometry, a comparison is made to image-domain SPS reconstruction using the Huber penalty. The effects of varying object size and contrast are also investigated. For the helical cone-beam geometry, we investigate the effect of helical pitch (axial movement/rotation). Huber-penalty sinogram restoration is performed on 3D clinical data, and the reconstructed images are compared to those generated with no restoration. Results: We find that by applying the edge-preserving Huber penalty to our sinogram restoration methods, the reconstructed image has a better resolution-noise relationship than an image produced using a quadratic penalty in the sinogram restoration. However, we find that this relatively straightforward approach to edge preservation in the sinogram domain is affected by the physical size of imaged objects in addition to the contrast across the edge. This presents some disadvantages of this method relative to image-domain edge-preserving methods, although the computational burden of the sinogram-domain approach is much lower. For a helical cone-beam geometry, we found applying sinogram restoration in 3D was reasonable and that pitch did not make a significant difference in the general effect of sinogram restoration. The application of Huber-penalty sinogram restoration to clinical data resulted in a reconstruction with less noise while retaining resolution. Conclusions: Sinogram restoration with the Huber penalty is able to provide better resolution-noise performance than restoration with a quadratic penalty. Additionally, sinogram restoration with the Huber penalty is feasible for helical cone-beam CT and can be applied to clinical data.« less

75 FR 9159 - Certain Helical Spring Lock Washers from the People's Republic of China: Extension of Time Limit...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-01

... DEPARTMENT OF COMMERCE International Trade Administration [A-570-822] Certain Helical Spring Lock... of the administrative review of the antidumping duty order on certain helical spring lock washers... September 30, 2008. See Certain Helical Spring Lock Washers from the People's Republic of China: Preliminary...

Godbillon Vey Helicity and Magnetic Helicity in Magnetohydrodynamics

NASA Astrophysics Data System (ADS)

Webb, G. M.; Hu, Q.; Anco, S.; Zank, G. P.

2017-12-01

The Godbillon-Vey invariant arises in homology theory, and algebraic topology, where conditions for a layered family of 2D surfaces forms a 3D manifold were elucidated. The magnetic Godbillon-Vey helicity invariant in magnetohydrodynamics (MHD) is a helicity invariant that occurs for flows, in which the magnetic helicity density hm= A\\cdotB=0 where A is the magnetic vector potential and B is the magnetic induction. Our purpose is to elucidate the evolution of the magnetic Godbillon-Vey field η =A×B/|A|2 and the Godbillon-Vey helicity hgv}= η \\cdot∇ × η in general MHD flows in which the magnetic helicity hm≠q 0. It is shown that hm acts as a source term in the Godbillon-Vey helicity transport equation, in which hm is coupled to hgv via the shear tensor of the background flow. The transport equation for hgv depends on the electric field potential ψ , which is related to the gauge for A, which takes its simplest form for the advected A gauge in which ψ =A\\cdot u where u is the fluid velocity.

The helical MreB cytoskeleton in Escherichia coli MC1000/pLE7 is an artifact of the N-Terminal yellow fluorescent protein tag.

PubMed

Swulius, Matthew T; Jensen, Grant J

2012-12-01

Based on fluorescence microscopy, the actin homolog MreB has been thought to form extended helices surrounding the cytoplasm of rod-shaped bacterial cells. The presence of these and other putative helices has come to dominate models of bacterial cell shape regulation, chromosome segregation, polarity, and motility. Here we use electron cryotomography to show that MreB does in fact form extended helices and filaments in Escherichia coli when yellow fluorescent protein (YFP) is fused to its N terminus but native (untagged) MreB expressed to the same levels does not. In contrast, mCherry fused to an internal loop (MreB-RFP(SW)) does not induce helices. The helices are therefore an artifact of the placement of the fluorescent protein tag. YFP-MreB helices were also clearly distinguishable from the punctate, "patchy" localization patterns of MreB-RFP(SW), even by standard light microscopy. The many interpretations in the literature of such punctate patterns as helices should therefore be reconsidered.

Helicity transformation under the collision and merging of two magnetic flux ropes

NASA Astrophysics Data System (ADS)

DeHaas, Timothy; Gekelman, Walter

2017-07-01

Magnetic helicity has become a useful tool in the analysis of astrophysical plasmas. Its conservation in the magnetohydrodynamic limit (and other fluid approaches) constrains the global behavior of large plasma structures. One such astrophysical structure is a magnetic flux rope: a tube-like, current-carrying plasma embedded in an external magnetic field. Bundles of these ropes are commonly observed in the near-earth environment and solar atmosphere. In this well-diagnosed experiment (three-dimensional measurements of ne, Te, Vp, B, J, E, and uflow), two magnetic flux ropes are generated in the Large Plasma Device at UCLA. These ropes are driven kink-unstable to trigger complex motion. As they interact, helicity conservation is examined in regions of reconnection. We examine (1) the transport of helicity and (2) the dissipation of the helicity. As the ropes move and the topology of the field lines diverge, a quasi-separatrix layer (QSL) is formed. As the QSL forms, magnetic helicity is dissipated within this region. At the same time, there is an influx of canonical helicity into the region such that the temporal derivative of magnetic helicity is zero.

Comparison of forcing functions in magnetohydrodynamics

NASA Astrophysics Data System (ADS)

McKay, Mairi E.; Linkmann, Moritz; Clark, Daniel; Chalupa, Adam A.; Berera, Arjun

2017-11-01

Results are presented of direct numerical simulations of incompressible, homogeneous magnetohydrodynamic turbulence without a mean magnetic field, subject to different mechanical forcing functions commonly used in the literature. Specifically, the forces are negative damping (which uses the large-scale velocity field as a forcing function), a nonhelical random force, and a nonhelical static sinusoidal force (analogous to helical ABC forcing). The time evolution of the three ideal invariants (energy, magnetic helicity, and cross helicity), the time-averaged energy spectra, the energy ratios, and the dissipation ratios are examined. All three forcing functions produce qualitatively similar steady states with regard to the time evolution of the energy and magnetic helicity. However, differences in the cross-helicity evolution are observed, particularly in the case of the static sinusoidal method of energy injection. Indeed, an ensemble of sinusoidally forced simulations with identical parameters shows significant variations in the cross helicity over long time periods, casting some doubt on the validity of the principle of ergodicity in systems in which the injection of helicity cannot be controlled. Cross helicity can unexpectedly enter the system through the forcing function and must be carefully monitored.

Helicity conservation by flow across scales in reconnecting vortex links and knots

PubMed Central

Scheeler, Martin W.; Kleckner, Dustin; Kindlmann, Gordon L.; Irvine, William T. M.

2014-01-01

The conjecture that helicity (or knottedness) is a fundamental conserved quantity has a rich history in fluid mechanics, but the nature of this conservation in the presence of dissipation has proven difficult to resolve. Making use of recent advances, we create vortex knots and links in viscous fluids and simulated superfluids and track their geometry through topology-changing reconnections. We find that the reassociation of vortex lines through a reconnection enables the transfer of helicity from links and knots to helical coils. This process is remarkably efficient, owing to the antiparallel orientation spontaneously adopted by the reconnecting vortices. Using a new method for quantifying the spatial helicity spectrum, we find that the reconnection process can be viewed as transferring helicity between scales, rather than dissipating it. We also infer the presence of geometric deformations that convert helical coils into even smaller scale twist, where it may ultimately be dissipated. Our results suggest that helicity conservation plays an important role in fluids and related fields, even in the presence of dissipation. PMID:25326419

Assembly of mesoscale helices with near-unity enantiomeric excess and light-matter interactions for chiral semiconductors

PubMed Central

Feng, Wenchun; Kim, Ji-Young; Wang, Xinzhi; Calcaterra, Heather A.; Qu, Zhibei; Meshi, Louisa; Kotov, Nicholas A.

2017-01-01

Semiconductors with chiral geometries at the nanoscale and mesoscale provide a rich materials platform for polarization optics, photocatalysis, and biomimetics. Unlike metallic and organic optical materials, the relationship between the geometry of chiral semiconductors and their chiroptical properties remains, however, vague. Homochiral ensembles of semiconductor helices with defined geometries open the road to understanding complex relationships between geometrical parameters and chiroptical properties of semiconductor materials. We show that semiconductor helices can be prepared with an absolute yield of ca 0.1% and an enantiomeric excess (e.e.) of 98% or above from cysteine-stabilized cadmium telluride nanoparticles (CdTe NPs) dispersed in methanol. This high e.e. for a spontaneously occurring chemical process is attributed to chiral self-sorting based on the thermodynamic preference of NPs to assemble with those of the same handedness. The dispersions of homochiral self-assembled helices display broadband visible and near-infrared (Vis-NIR) polarization rotation with anisotropy (g) factors approaching 0.01. Calculated circular dichroism (CD) spectra accurately reproduced experimental CD spectra and gave experimentally validated spectral predictions for different geometrical parameters enabling de novo design of chiroptical semiconductor materials. Unlike metallic, ceramic, and polymeric helices that serve predominantly as scatterers, chiroptical properties of semiconductor helices have nearly equal contribution of light absorption and scattering, which is essential for device-oriented, field-driven light modulation. Deconstruction of a helix into a series of nanorods provides a simple model for the light-matter interaction and chiroptical activity of helices. This study creates a framework for further development of polarization-based optics toward biomedical applications, telecommunications, and hyperspectral imaging. PMID:28275728

Common and divergent structural features of a series of corticotropin releasing factor-related peptides.

PubMed

Grace, Christy Rani R; Perrin, Marilyn H; Cantle, Jeffrey P; Vale, Wylie W; Rivier, Jean E; Riek, Roland

2007-12-26

Members of the corticoliberin family include the corticotropin releasing factors (CRFs), sauvagine, the urotensins, and urocortin 1 (Ucn1), which bind to both the CRF receptors CRF-R1 and CRF-R2, and the urocortins 2 (Ucn2) and 3 (Ucn3), which are selective agonists of CRF-R2. Structure activity relationship studies led to several potent and long-acting analogues with selective binding to either one of the receptors. NMR structures of six ligands of this family (the antagonists astressin B and astressin2-B, the agonists stressin1, and the natural ligands human Ucn1, Ucn2, and Ucn3) were determined in DMSO. These six peptides show differences in binding affinities, receptor-selectivity, and NMR structure. Overall, their backbones are alpha-helical, with a small kink or a turn around residues 25-27, resulting in a helix-loop-helix motif. The C-terminal helices are of amphipathic nature, whereas the N-terminal helices vary in their amphipathicity. The C-terminal helices thereby assume a conformation very similar to that of astressin bound to the ECD1 of CRF-R2 recently reported by our group.1 On the basis of an analysis of the observed 3D structures and relative potencies of [Ala]-substituted analogues, it is proposed that both helices could play a crucial role in receptor binding and selectivity. In conclusion, the C-terminal helices may interact along their hydrophobic faces with the ECD1, whereas the entire N-terminal helical surface may be involved in receptor activation. On the basis of the common and divergent features observed in the 3D structures of these ligands, multiple binding models are proposed that may explain their plurality of actions.

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

PubMed Central

2015-01-01

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

Optimization of view weighting in tilted-plane-based reconstruction algorithms to minimize helical artifacts in multi-slice helical CT

NASA Astrophysics Data System (ADS)

Tang, Xiangyang

2003-05-01

In multi-slice helical CT, the single-tilted-plane-based reconstruction algorithm has been proposed to combat helical and cone beam artifacts by tilting a reconstruction plane to fit a helical source trajectory optimally. Furthermore, to improve the noise characteristics or dose efficiency of the single-tilted-plane-based reconstruction algorithm, the multi-tilted-plane-based reconstruction algorithm has been proposed, in which the reconstruction plane deviates from the pose globally optimized due to an extra rotation along the 3rd axis. As a result, the capability of suppressing helical and cone beam artifacts in the multi-tilted-plane-based reconstruction algorithm is compromised. An optomized tilted-plane-based reconstruction algorithm is proposed in this paper, in which a matched view weighting strategy is proposed to optimize the capability of suppressing helical and cone beam artifacts and noise characteristics. A helical body phantom is employed to quantitatively evaluate the imaging performance of the matched view weighting approach by tabulating artifact index and noise characteristics, showing that the matched view weighting improves both the helical artifact suppression and noise characteristics or dose efficiency significantly in comparison to the case in which non-matched view weighting is applied. Finally, it is believed that the matched view weighting approach is of practical importance in the development of multi-slive helical CT, because it maintains the computational structure of fan beam filtered backprojection and demands no extra computational services.

Intracellular segment between transmembrane helices S0 and S1 of BK channel α subunit contains two amphipathic helices connected by a flexible loop

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

Shi, Pan; High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui, 230031; Li, Dong

2013-08-02

Highlights: •The loop between S0 and S1 of BK channel was overexpressed and purified in DPC. •NMR studies indicated BK-IS1 contained two helices connected by a flexible loop. •Mg{sup 2+} titration of BK-IS1 indicated two possible binding sites of divalent ions. -- Abstract: The BK channel, a tetrameric potassium channel with very high conductance, has a central role in numerous physiological functions. The BK channel can be activated by intracellular Ca{sup 2+} and Mg{sup 2+}, as well as by membrane depolarization. Unlike other tetrameric potassium channels, the BK channel has seven transmembrane helices (S0–S6) including an extra helix S0. Themore » intracellular segment between S0 and S1 (BK-IS1) is essential to BK channel functions and Asp99 in BK-IS1 is reported to be responsible for Mg{sup 2+} coordination. In this study, BK-IS1 (44–113) was over-expressed using a bacterial system and purified in the presence of detergent micelles for multidimensional heteronuclear nuclear magnetic resonance (NMR) structural studies. Backbone resonance assignment and secondary structure analysis showed that BK-IS1 contains two amphipathic helices connected by a 36-residue loop. Amide {sup 1}H–{sup 15}N heteronuclear NOE analysis indicated that the loop is very flexible, while the two amphipathic helices are possibly stabilized through interaction with the membrane. A solution NMR-based titration assay of BK-IS1 was performed with various concentrations of Mg{sup 2+}. Two residues (Thr45 and Leu46) with chemical shift changes were observed but no, or very minor, chemical shift difference was observed for Asp99, indicating a possible site for binding divalent ions or other modulation partners.« less

A helical biosonar scanning pattern in the Chinese noctule, Nyctalus plancyi.

PubMed

Müller, Rolf; Lu, Hongwang; Zhang, Shuyi; Peremans, Herbert

2006-06-01

Directivity and sound diffraction of the pinna of the Chinese Noctule (Nyctalus plancyi) have been studied numerically. The pinna was found capable of generating a periodic helical scanning pattern over frequency, if the tragus and the thickened lower ledge of the pinna rim were in an appropriate position. During the helical scan, a directivity pattern with a strong mainlobe alternated with a pattern dominated by a conical sleeve of sidelobes. This alternation was present, even when an unfavorable arrangement of the pinna disrupted the overall helical scanning pattern. In the fully formed helical scan, the orientation of main and sidelobes for different frequencies revealed a spatial ordering which extends volume coverage. Five different pinna parts have been removed from the digital pinna-shape representations in turn to assess their influence on the directivity. Of these parts, the tragus stem and the thickened lower ledge of the pinna rim were found to have the largest overall impact. The anatomical prominence of these structures was hence in agreement with their acoustic functionality. In the near-field, tragus stem and lower ledge were seen to act primarily through large shifts in the wavefield phase in both directions.

Magnetic Energy and Helicity in Two Emerging Active Regions in the Sun

NASA Technical Reports Server (NTRS)

Liu, Y.; Schuck, P. W.

2012-01-01

The magnetic energy and relative magnetic helicity in two emerging solar active regions, AR 11072 and AR 11158,are studied. They are computed by integrating over time the energy and relative helicity fluxes across the photosphere. The fluxes consist of two components: one from photospheric tangential flows that shear and braid field lines (shear term), the other from normal flows that advect magnetic flux into the corona (emergence term). For these active regions: (1) relative magnetic helicity in the active-region corona is mainly contributed by the shear term,(2) helicity fluxes from the emergence and the shear terms have the same sign, (3) magnetic energy in the corona (including both potential energy and free energy) is mainly contributed by the emergence term, and(4) energy fluxes from the emergence term and the shear term evolved consistently in phase during the entire flux emergence course.We also examine the apparent tangential velocity derived by tracking field-line footpoints using a simple tracking method. It is found that this velocity is more consistent with tangential plasma velocity than with the flux transport velocity, which agrees with the conclusion by Schuck.

Electromagnetic absorption behaviour of ferrite loaded three phase carbon fabric composites

NASA Astrophysics Data System (ADS)

Jagatheesan, Krishnasamy; Ramasamy, Alagirusamy; Das, Apurba; Basu, Ananjan

2018-02-01

This article investigates the electromagnetic absorption behaviours of carbon helical yarn fabric reinforced composites and manganese-zinc (Mn-Zn) ferrite particles loaded 3 phase fabric composites. A carbon helical yarn having stainless steel core was prepared and made into single jersey knitted fabric. The composite was prepared by sandwiching a fabric with polypropylene films and thermal pressed. The absorption values of helical yarn fabric composite was observed to be less in the C band region (4-8 GHz). For improving the absorption coefficients of composite, Mn-Zn ferrite particles were dispersed in the polypropylene (PP) composite. The ferrite loaded PP composites exhibited better permittivity and permeability values, hence the absorption loss of the composite was improved. The helical yarn fabric reinforced with Mn-Zn ferrite/PP composite showed larger absorption coefficients than virgin PP/fabric composite. The change in thermal stability and particle size distribution in the Mn-Zn ferrite/PP composite was also analyzed. At higher ferrite concentration, bimodal particle distribution was observed which increased the conductivity and shielding effectiveness (SE) of the composite. In addition, complex permittivity value was also increased for higher incident frequency (4-8 GHz). As the ferrite content increases, the dielectric loss and magnetic permeability of PP/ferrite increases due to increased magnetic loss. Hence, ferrite loaded PP composite showed the total SE of -14.2 dB with the absorption coefficients of 0.717. The S1C7 fabric composite having ferrite dispersion showed the better absorption loss and lower reflection coefficient of 14.2 dB and 0.345 respectively compared to virgin PP/helical yarn fabric composite. The increasing ferrite content (45 wt%) improved the absorption loss and total SE. Though, ferrite based fabric composite exhibits moderate absorptive shielding, it can be used as shielding panels in the electronic industries.

From neutral to zwitterionic poly(α-amino acid) nonfouling surfaces: Effects of helical conformation and anchoring orientation.

PubMed

Zhang, Chong; Yuan, Jingsong; Lu, Jianhua; Hou, Yingqin; Xiong, Wei; Lu, Hua

2018-02-03

The development of high-performance nonfouling polymer surfaces for implantable medical devices and therapeutic nanomaterials is of great importance. Elaborating the relationship of polymer structural characteristics and the resulted surface properties can offer useful guidance toward ideal biointerfaces. In this work, we investigate the effects of the helical conformation and anchoring orientation of poly(α-amino acid)s (PαAAs) to produce advanced nonfouling surfaces. By using the neutral poly(γ-(2-(2-(2-methoxyethoxy)ethoxy)ethoxy)esteryl glutamates) (P(EG 3 Glu)s) as a model system, the adsorption kinetics are monitored by ex-situ variable angle spectroscopic ellipsometry and in-situ quartz crystal microbalance with dissipation. It is found that the polymers adopting a rigid rod-like α-helical conformation can self-assemble more rapidly to produce denser adlayers, and generate significantly improved nonfouling surfaces compared to those flexible polymer analogues including the widely used antifouling polymer PEG. Moreover, the surface properties can be further enhanced by using the antiparallel orientated helical P(EG 3 Glu)s. Most importantly, the insights gained from the P(EG 3 Glu) model system are successfully applied to the generation of ultra-low-fouling surfaces using zwitterionic PαAAs brushes, underscoring the generality of the approach. Particularly, the surface based on the antiparallel aligned zwitterionic helical PαAAs exhibits ∼98-99% reduction of human serum adsorption relative to the bare gold, and gives almost no adhesion of mouse platelet. Taken together, this work depicts an extremely simple yet highly effective approach to manipulate surface properties for numerous applications in biomaterial interfaces, diagnostics, and biosensors. Copyright © 2018 Elsevier Ltd. All rights reserved.

Structural effects of extracellular loop mutations in CFTR helical hairpins.

PubMed

Chang, Yuan-Heng; Stone, Tracy A; Chin, Stephanie; Glibowicka, Mira; Bear, Christine E; Deber, Charles M

2018-05-01

Missense mutations constitute 40% of 2000 cystic fibrosis-phenotypic mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) database, yet the precise mechanism as to how a point mutation can render the entire 1480-residue CFTR protein dysfunctional is not well-understood. Here we investigate the structural effects of two CF-phenotypic mutations - glutamic acid to glycine at position 217 (E217G) and glutamine to arginine at position 220 (Q220R) - in the extracellular (ECL2) loop region of human CFTR using helical hairpin constructs derived from transmembrane (TM) helices 3 and 4 of the first membrane domain. We systematically replaced the wild type (WT) residues E217 and Q220 with the subset of missense mutations that could arise through a single nucleotide change in their respective codons. Circular dichroism spectra of E217G revealed that a significant increase in helicity vs. WT arises in the membrane-mimetic environment of sodium dodecylsulfate (SDS) micelles, while this mutant showed a similar gel shift to WT on SDS-PAGE gels. In contrast, the CF-mutant Q220R showed similar helicity but an increased gel shift vs. WT. These structural variations are compared with the maturation levels of the corresponding mutant full-length CFTRs, which we found are reduced to approx. 50% for E217G and 30% for Q220R vs. WT. The overall results with CFTR hairpins illustrate the range of impacts that single mutations can evoke in intramolecular protein-protein and/or protein-lipid interactions - and the levels to which corresponding mutations in full-length CFTR may be flagged by quality control mechanisms during biosynthesis. Copyright © 2018 Elsevier B.V. All rights reserved.

Secondary Structural Changes of Intact and Disulfide Bridges-Cleaved Human Serum Albumins in Thermal Denaturation up to 130°C - Additive Effects of Sodium Dodecyl Sulfate on the Changes.

PubMed

Moriyama, Yoshiko; Takeda, Kunio

2017-05-01

The secondary structural changes of human serum albumin with the intact 17 disulfide bridges (HSA) and the disulfide bridges-cleaved human serum albumin (RCM-HSA) in thermal denaturation were examined. Most of the helical structures of HSA, whose original helicity was 66%, were sharply disrupted between 50 and 100°C. However, 14% helicity remained even at 130°C. The temperature dependence of the degree of disrupted helical structures of HSA was discussed in connection with questions about a general protein denaturation model. When HSA lost the disulfide bridges, about two-thirds of the original helices were disrupted. Although the helices of RCM-HSA remaining after the cleavage of the disulfide bridges were relatively resistant against the heat treatment, the helicity changed from 22% at 25°C to 14% at 130℃. The helicity of RCM-HSA at 130°C agreed with the helicity of HSA at the same temperature, indicating that the same helical moieties of the polypeptides remained unaffected at this high temperature. The additive effects of sodium dodecyl sulfate (SDS) on the structural changes of HSA and RCM-HSA in thermal denaturation were also examined. A slight amount of SDS protected the helical structures of HSA from thermal denaturation below 80°C. Upon cooling to 25°C after heat treatment at temperatures below 70°C with the coexistence of SDS of low concentrations, the helical structures of HSA were reformed to the original level at 25°C before heating. A similar tendency was also observed after heat treatment at 80°C. In contrast, the helical structures of the RCM-HSA complexes with SDS are completely recovered upon cooling to 25°C even after heat treatment up to 100°C. Similar investigations were also carried out on bovine serum albumins which had the intact 17 disulfide bridges and lost all of the bridges.

Ultrasound SIV measurement of helical valvular flow behind the great saphenous vein

NASA Astrophysics Data System (ADS)

Park, Jun Hong; Kim, Jeong Ju; Lee, Sang Joon; Yeom, Eunseop; Experimental Fluid Mechanics Laboratory Team; LaboratoryMicrothermal; Microfluidic Measurements Collaboration

2017-11-01

Dysfunction of venous valve and induced secondary abnormal flow are closely associated with venous diseases. Thus, detailed analysis of venous valvular flow is invaluable from biological and medical perspectives. However, most previous studies on venous perivalvular flows were based on qualitative analyses. On the contrary, quantitative analysis on the perivalvular flows has not been fully understood yet. In this study, 3D valvular flows under in vitro and in vivo conditions were experimentally investigated using ultrasound speckle image velocimetry (SIV) for analyzing their flow characteristics. The results for in vitro model obtained by the SIV technique were compared with those derived by numerical simulation and color Doppler method to validate its measurement accuracy. Then blood flow in the human great saphenous vein was measured using the SIV with respect to the dimensionless index, helical intensity. The results obtained by the SIV method are well matched well with those obtained by the numerical simulation and color Doppler method. The hemodynamic characteristics of 3D valvular flows measured by the validated SIV method would be helpful in diagnosis of valve-related venous diseases. None.

Cryogenic High-Pressure Shear-Coaxial Jets Exposed to Transverse Acoustic Forcing

DTIC Science & Technology

2011-12-13

formation. Detailed studies on the development and growth of natural instabilities in a single circular jet6 or a single circular jet with coflow7...reveal two of the most significant natural modes of instability: the axisymmetric and the first azimuthal or helical modes. These modes have comparable... natural as well as externally imposed flow conditions such as pressure or velocity perturbations, affecting their development, may be used to assess

Ambipolar diffusion drifts and dynamos in turbulent gases

NASA Technical Reports Server (NTRS)

Zweibel, Ellen G.

1988-01-01

Ambipolar drift in turbulent fluids are considered. Using mean-field electrodynamics, a two-scale theory originally used to study hydromagnetic dynamos, it is shown that magnetic fields can be advected by small-scale magnetosonic (compressional) turbulence or generated by Alfvenic (helical) turbulence. A simple dynamo theory is made and is compared with standard theories in which dissipation is caused by turbulent diffusion. The redistribution of magnetic flux in interstellar clouds is also discussed.

Spinor helicity methods in high-energy factorization: Efficient momentum-space calculations in the Color Glass Condensate formalism

NASA Astrophysics Data System (ADS)

Ayala, Alejandro; Hentschinski, Martin; Jalilian-Marian, Jamal; Tejeda-Yeomans, Maria Elena

2017-07-01

We use the spinor helicity formalism to calculate the cross section for production of three partons of a given polarization in Deep Inelastic Scattering (DIS) off proton and nucleus targets at small Bjorken x. The target proton or nucleus is treated as a classical color field (shock wave) from which the produced partons scatter multiple times. We reported our result for the final expression for the production cross section and studied the azimuthal angular correlations of the produced partons in [1]. Here we provide the full details of the calculation of the production cross section using the spinor helicity methods.

Electromagnetic duality and the electric memory effect

NASA Astrophysics Data System (ADS)

Hamada, Yuta; Seo, Min-Seok; Shiu, Gary

2018-02-01

We study large gauge transformations for soft photons in quantum electrodynamics which, together with the helicity operator, form an ISO(2) algebra. We show that the two non-compact generators of the ISO(2) algebra correspond respectively to the residual gauge symmetry and its electromagnetic dual gauge symmetry that emerge at null infinity. The former is helicity universal (electric in nature) while the latter is helicity distinguishing (magnetic in nature). Thus, the conventional large gauge transformation is electric in nature, and is naturally associated with a scalar potential. We suggest that the electric Aharonov-Bohm effect is a direct measure for the electromagnetic memory arising from large gauge transformations.

Fiber-guided modes conversion using superposed helical gratings

NASA Astrophysics Data System (ADS)

Ma, Yancheng; Fang, Liang; Wu, Guoan

2017-03-01

Optical fibers can support various modal forms, including vector modes, linear polarization (LP) modes, and orbital angular momentum (OAM) modes, etc. The modal correlation among these modes is investigated via Jones matrix, associated with polarization and helical phase corresponding to spin angular momentum (SAM) and OAM of light, respectively. We can generate different modal forms by adopting superposed helical gratings (SHGs) with opposite helix orientations. Detailed analysis and discussion on mode conversion is given as for mode coupling in optical fibers with both low and high contrast index, respectively. Our study may deepen the understanding for various fiber-guided modes and mode conversion among them via fiber gratings.

Cascade unlooping of a low-pitch helical spring under tension

NASA Astrophysics Data System (ADS)

Starostin, E. L.; van der Heijden, G. H. M.

2009-06-01

We study the force vs. extension behaviour of a helical spring made of a thin torsionally stiff anisotropic elastic rod. Our focus is on springs of very low helical pitch. For certain parameters of the problem such a spring is found not to unwind when pulled but rather to form hockles that pop out one by one and lead to a highly non-monotonic force-extension curve. Between abrupt loop pop-outs this curve is well described by the planar elastica whose relevant solutions are classified. Our results may be relevant for tightly coiled nanosprings in future micro- and nano(electro)mechanical devices.

Magnetic dynamo action at low magnetic Prandtl numbers.

PubMed

Malyshkin, Leonid M; Boldyrev, Stanislav

2010-11-19

Amplification of magnetic field due to kinematic turbulent dynamo action is studied in the regime of small magnetic Prandtl numbers. Such a regime is relevant for planets and stars interiors, as well as for liquid-metal laboratory experiments. A comprehensive analysis based on the Kazantsev-Kraichnan model is reported, which establishes the dynamo threshold and the dynamo growth rates for varying kinetic helicity of turbulent fluctuations. It is proposed that in contrast with the case of large magnetic Prandtl numbers, the kinematic dynamo action at small magnetic Prandtl numbers is significantly affected by kinetic helicity, and it can be made quite efficient with an appropriate choice of the helicity spectrum.

Supramolecular self-assemblies of beta-cyclodextrins with aromatic tethers: factors governing the helical columnar versus linear channel superstructures.

PubMed

Liu, Yu; Fan, Zhi; Zhang, Heng-Yi; Yang, Ying-Wei; Ding, Fei; Liu, Shuang-Xi; Wu, Xue; Wada, Takehiko; Inoue, Yoshihisa

2003-10-31

A series of 6-O-(p-substituted phenyl)-modified beta-cyclodextrin derivatives, i.e., 6-O-(4-bromophenyl)-beta-CD (1), 6-O-(4-nitrophenyl)-beta-CD (2), 6-O-(4-formylphenyl)-beta-CD (3), 6-phenylselenyl-6-deoxy-beta-CD (4), and 6-O-(4-hydroxybenzoyl)-beta-CD (5), were synthesized, and their inclusion complexation behavior in aqueous solution and self-assembling behavior in the solid state were comparatively studied by NMR spectroscopy, microcalorimetry, crystallography, and scanning tunneling microscopy. Interestingly, (seleno)ethers 1-4 and ester 5 displayed distinctly different self-assembling behavior in the solid state, affording a successively threading head-to-tail polymeric helical structure for the (seleno)ethers or a mutually penetrating tail-to-tail dimeric columnar channel structure for the ester. Combining the present and previous structures reported for the relevant beta-CD derivatives, we further deduce that the pivot heteroatom, through which the aromatic substituent is tethered to beta-CD, plays a critical role in determining the helix structure, endowing the 2-fold and 4-fold axes to the N/O- and S/Se-pivoted beta-CD aggregates, respectively. This means that one can control the self-assembling orientation, alignment, and helicity in the solid state by finely tuning the pivot atom and the tether length. Further NMR and calorimetric studies on the self-assembling behavior in aqueous solution revealed that the dimerization step is the key to the formation of linear polymeric supramolecular architecture, which is driven by favorable entropic contributions.

Instabilities of a rotating helical rod

NASA Astrophysics Data System (ADS)

Park, Yunyoung; Ko, William; Kim, Yongsam; Lim, Sookkyung

2016-11-01

Bacteria such as Escherichia coli and Vibrio alginolyticus have helical flagellar filament. By rotating a motor, which is located at the bottom end of the flagellar filament embedded in the cell body, CCW or CW, they swim forward or backward. We model a left-handed helix by the Kirchhoff rod theory and use regularized Stokes formulation to study an interaction between the surrounding fluid and the flagellar filament. We perform numerical studies focusing on relations between physical parameters and critical angular frequency of the motor, which separates overwhiring from twirling. We are also interested in the buckling instability of the hook, which is very flexible elastic rod. By measuring buckling angle, which is an angle between rotational axis and helical axis, we observe the effects of physical parameters on buckling of the hook.

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.

Properties of polyproline II, a secondary structure element implicated in protein-protein interactions.

PubMed

Cubellis, M V; Caillez, F; Blundell, T L; Lovell, S C

2005-03-01

The polyproline II (PPII) conformation of protein backbone is an important secondary structure type. It is unusual in that, due to steric constraints, its main-chain hydrogen-bond donors and acceptors cannot easily be satisfied. It is unable to make local hydrogen bonds, in a manner similar to that of alpha-helices, and it cannot easily satisfy the hydrogen-bonding potential of neighboring residues in polyproline conformation in a manner analogous to beta-strands. Here we describe an analysis of polyproline conformations using the HOMSTRAD database of structurally aligned proteins. This allows us not only to determine amino acid propensities from a much larger database than previously but also to investigate conservation of amino acids in polyproline conformations, and the conservation of the conformation itself. Although proline is common in polyproline helices, helices without proline represent 46% of the total. No other amino acid appears to be greatly preferred; glycine and aromatic amino acids have low propensities for PPII. Accordingly, the hydrogen-bonding potential of PPII main-chain is mainly satisfied by water molecules and by other parts of the main-chain. Side-chain to main-chain interactions are mostly nonlocal. Interestingly, the increased number of nonsatisfied H-bond donors and acceptors (as compared with alpha-helices and beta-strands) makes PPII conformers well suited to take part in protein-protein interactions. Copyright 2005 Wiley-Liss, Inc.