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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
NASA NTRS2000

Molecular View of Protein Crystal Growth: Molecular Interactions, Surface Reconstruction and Growth Mechanism

Studies of the growth and molecular packing of tetragonal lysozyme crystals suggest that there is an underlying molecular growth mechanism, in addition to the classical one involving screw dislocation/2D) nucleation growth. These crystals are constructed by strongly bonded molecular chains forming helices about the 43 axes. The helices are connected to each other by weaker bonds. Crystal growth proceeds by the formation of these 4(sub 3) helices, which would explain some unexpected observations by earlier investigators, such as bimolecular growth steps on the (110) face. Another consequence of these molecular considerations is that only one of two possible packing arrangements could occur on the crystal faces and that their growth unit was at least a tetramer corresponding to the 4(sub 3) helix. Two new high resolution atomic force microscopy (AFM) techniques were developed to directly confirm these predictions on tetragonal lysozyme crystals. Most earlier investigations of protein crystal growth with AFM were in the low resolution mode which is adequate to investigate the classical growth mechanisms, but cannot resolve molecular features and mechanisms. Employing the first of the newly developed techniques, high resolution AFM images of the (110) face were compared with the theoretically constructed images for the two possible packing arrangements on this face. The prediction that the molecular packing arrangement of these faces corresponded to that for complete 4(sub 3) helices was confirmed in this manner. This investigation also showed the occurrence of surface reconstruction on protein crystals. The molecules on the surface of the (110) face were found to pack closer along the 4(sub 3) axes than those in the interior. The second new AFM technique was used to follow the growth process by measuring the dimensions of individual growth units on the (110) face. Linescans across a growth step, performed near the saturation limit of the crystals, allowed the growth unit dimensions to be measured as they were being incorporated into the crystal. These measurements showed that growth on the (110) face proceeded by the formation of new 4(sub 3) helices from the addition of many growth units of at least tetramer size. This is the first time that a time-resolved AFM technique has been used to observe individual molecular events during crystal growth.

Nadarajah, Arunan↗
NASA NTRS2001

Structural models of the MscL gating mechanism

Three-dimensional structural models of the mechanosensitive channel of large conductance, MscL, from the bacteria Mycobacterium tuberculosis and Escherichia coli were developed for closed, intermediate, and open conformations. The modeling began with the crystal structure of M. tuberculosis MscL, a homopentamer with two transmembrane alpha-helices, M1 and M2, per subunit. The first 12 N-terminal residues, not resolved in the crystal structure, were modeled as an amphipathic alpha-helix, called S1. A bundle of five parallel S1 helices are postulated to form a cytoplasmic gate. As membrane tension induces expansion, the tilts of M1 and M2 are postulated to increase as they move away from the axis of the pore. Substantial expansion is postulated to occur before the increased stress in the S1 to M1 linkers pulls the S1 bundle apart. During the opening transition, the S1 helices and C-terminus amphipathic alpha-helices, S3, are postulated to dock parallel to the membrane surface on the perimeter of the complex. The proposed gating mechanism reveals critical spatial relationships between the expandable transmembrane barrel formed by M1 and M2, the gate formed by S1 helices, and "strings" that link S1s to M1s. These models are consistent with numerous experimental results and modeling criteria.

NASA Discipline Cell Biology↗
NASA NTRS1982

Noise of the 10-bladed, 40 deg swept SR-6 propeller in a wind tunnel

The noise generated by supersonic helical-tip-speed propellers is a likely cabin environment problem for future airplanes powered by these propellers. Three propeller models with different tip sweeps. SR-1M, SR-2, and SR-3, designed for 244 m/sec (800 ft/sec) tip speed at a flight Mach number of 0.8 were previously tested in the NASA Lewis 8- by 6-Foot Wind Tunnel. In order to investigated another design point condition, the SR-6 propeller was designed for 213 m-sec (700 ft/sec) tip speed at a flight Mach number of 0.8. The noise data from this propeller are reported herein. Curves of blade passing frequency noise versus tip Mach number (at constant advance ratio) showed that the SR-6 propeller behaved similarly to the SR-1M propeller. The noise of the SR-6 propeller at its design condition, helical tip Mach number of 1.07, is approximately 3 dB quieter than the SR-2 propeller at its higher design helical tip Mach number of 1.15, but about 2.5 dB noisier than SR-3 at its design condition. The helical tip Mach number shift of the steep noise rise followed the same progression as the blade sweep angle for all of the propellers. When operated at the SR-3 design point, the SR-6 propeller was approximately 1.5 dB quieter than SR-2 and 4 dB noisier than SR-3.

Dittmar, J. H.↗
NASA NTRS1983

Noise of the 10-bladed 60 deg swept SR-5 propeller in a wind tunnel

Noise generated by supersonic helical tip speed propellers is a possible cabin environment problem for future airplanes powered by these propellers. Noise characteristics of one of these propellers, designated SR-5, are presented. A matrix of tests was conducted to provide as much acoustic information as possible. During aerodynamic testing it was discovered that the propeller had an aeroelastic instability which prevented testing the propeller at its design advance ratio of 4.08 at axial Mach numbers over 0.7. Plots of the variation of the maximum blade passage tone with helical tip Mach number indicate that, at higher helical tip Mach numbers, the propeller operated on sharply increasing portion of the noise curve; therefore, extrapolations to the design condition would not be accurate. A possible extrapolation indicated that SR-5 at its design point should be quieter than SR-3 at its design point. Directivity plots at the higher helical tip Mach numbers indicate a lobed directivity pattern as was observed previously on the SR-3 propeller.

Dittmar, J. H.↗
NASA NTRS1983

Determining the alpha dynamo parameter in incompressible homogeneous magnetohydrodynamic turbulence

Alpha, an important parameter in dynamo theory, is proportional to either the kinetic, current, magnetic, or velocity helicity of the fluctuating magnetic field and fluctuating velocity field. The particular helicity to which alpha is proportional depends on the assumptions used in deriving the first order smoothed equations that describe the alpha effect. In two cases, when alpha is proportional to either the magnetic helicity or velocity helicity, alpha is determined experimentally from two point measurements of the fluctuating fields in incompressible, homogeneous turbulence having arbitrary symmetry. For the other two possibilities, alpha is determined if the turbulence is isotropic.

Matthaeus, W. H.↗
NASA NTRS1984

Orbital stability in combined uniform axial and three-dimensional wiggler magnetic fields for free-electron lasers

Zachary Phys. Rev. A 29 (6), 3224 (1984) recently analyzed the instability of relativistic-electron helical trajectories in combined uniform axial and helical wiggler magnetic fields when the radial variation of the wiggler field is taken into account. It is shown here that the type 2 instability comprised of secular terms growing linearly in time, identified by Zachary and earlier by Diament Phys. Rev. A 23 (5), 2537 (1981), is an artifact of simple perturbation theory. A multiple-time-scale perturbation analysis reveals a nonsecular evolution on a slower time scale which accommodates an arbitrary initial perturbation. It is shown that, in the absence of exponential instability, the electron seeks a modified helical orbit more appropriate to its perturbed state and oscillates stably about it. Thus, the perturbed motion is oscillatory but nonsecular, and hence the helical orbits are stable.

Johnston, S.↗
NASA NTRS1986

Multi-path peristaltic pump

The instant invention is directed to a peristaltic pump for critical laboratory or hospital applications requiring precise flow rates over an extended period of time. Within the cylindrical barrel pump housing is a single-piece, molded, elastometric, cylindrical liner with a multiplicity of flattened helical channels created therein from one end of the liner to the other. Three cylindrical rollers rotate about the center axis of the pump around the inside surface of the liner selectively compressing the liner, and hence the helical channels between the rollers and the barrel housing, creating a pumping action by forcing trapped fluid in the helical channels axially from one end of the liner to the opposite end. The novelty of the invention appears to lie in the provision of the special liner with multiple helical channels as the pumping chamber, rather than the standard single elastomeric tubing which is squeezed repeatedly by rollers to move the liquid through a typical peristaltic pump. Large, repeated deflections on the standard tubing causes a permanent set in the tubing, thus either changing the flow rate, or requiring a new section of tubing to be positioned in the pump head. Further, this configuration minimizes the amount of outflow pulsation which is characteristic of a typical single tubing peristaltic pump.

Chandler, Joseph A.↗
NASA NTRS1987

Expansion of epicyclic gear dynamic analysis program

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

Boyd, Linda Smith↗
NASA NTRS1989

Cruise noise of the SR-2 propeller model in a wind tunnel

Noise data on the SR-2 model propeller were taken in the NASA Lewis Research Center 8- by 6-Foot Wind Tunnel. The maximum blade passing tone rises with increasing helical tip Mach number to a peak level at a helical tip Mach number of about 1.05; then it remains the same or decreases at higher helical tip Mach numbers. This behavior, which has been observed with other propeller models, points to the possibility of using higher propeller tip speeds to limit airplane cabin noise while maintaining high flight speed and efficiency. Noise comparisons of the straight-blade SR-2 propeller and the swept-blade SR-7A propeller showed that the tailored sweep of the SR-7A appears to be the cause of both lower peak noise levels and a slower noise increase with increasing helical tip Mach number.

Dittmar, James H.↗
NASA NTRS1989

Formation and eruption of solar prominences

A model for the magnetic field associated with solar prominences is considered. It is shown that flux cancellation at the neutral line of a sheared magnetic arcade leads to the formation of helical field lines which are capable, in principle, of supporting prominence plasma. A numerical method for the computation of force-free, canceling magnetic structures is presented. Starting from an initial potential field we prescribe the motions of magnetic footpoints at the photosphere, with reconnection occurring only at the neutral line. As more and more flux cancels, magnetic flux is transferred from the arcade field to the helical field. Results for a particular model of the photospheric motions are presented. The magnetic structure is found to be stable: the arcade field keeps the helical field tied down at the photosphere. The axis of the helical field moves to larger and larger height, suggestive of prominence eruption. These results suggest that prominence eruptions may be trigered by flux cancellation.

Van Ballegooijen, A. A.↗
NASA NTRS1995

Computerized Design and Generation of Low-Noise Gears with Localized Bearing Contact

The results of research projects directed at the reduction of noise caused by misalignment of the following gear drives: double-circular arc helical gears, modified involute helical gears, face-milled spiral bevel gears, and face-milled formate cut hypoid gears are presented. Misalignment in these types of gear drives causes periodic, almost linear discontinuous functions of transmission errors. The period of such functions is the cycle of meshing when one pair of teeth is changed for the next. Due to the discontinuity of such functions of transmission errors high vibration and noise are inevitable. A predesigned parabolic function of transmission errors that is able to absorb linear discontinuous functions of transmission errors and change the resulting function of transmission errors into a continuous one is proposed. The proposed idea was successfully tested using spiral bevel gears and the noise was reduced a substantial amount in comparison with the existing design. The idea of a predesigned parabolic function is applied for the reduction of noise of helical and hypoid gears. The effectiveness of the proposed approach has been investigated by developed TCA (tooth contact analysis) programs. The bearing contact for the mentioned gears is localized. Conditions that avoid edge contact for the gear drives have been determined. Manufacturing of helical gears with new topology by hobs and grinding worms has been investigated.

Litvin, Faydor L.↗
NASA NTRS1994

Coalescence of two current loops with a kink instability simulated by a three-dimensional electromagnetic particle code

We have studied the dynamics of a coalescence of current loops using three-dimensional electromagnetic (EM) particle simulation code. Our focus is the investigation of such kinetic processes as energy trasnfer, heating particles, and electromagnetic emissions associated with a current loop coalescence which cannot be studied by MHD simulations. First, the two loops undergo a pinching oscillation due to a pressure imbalance between the inside and outside of the current loop. During the pinching oscillation, a kinetic kink instability is excited and electrons in the loops are heated perpendicularly to an ambient magnetic field. Next, the two current loops collide and coalesce, while at the same time a helical structure grows further. Subsequently, the perturbed current, which is due to these helically bunched electrons, can drive a whistler instability. It should be noted in this case that the whistler wave is excited by the kinetic kink instability and not a beam instability. After the coalescence of two helical loops, tilting motions can be observed in the direction of left-hand rotation, and the helical structure will relax resulting in strong plasma heating mostly in the direction perpendicular to the ambient magnetic field. It is also shown that high-frequency electromagnetic waves can be emitted from the region where the two loops coalesce and propagate strongly in the direction of the electron drift velocity. These processes may be important in understanding heating mechansims for coronal loops as well as radio wave emission mechanisms from active regions of solar plasmas.

Nishikawa, K.-I.↗
NASA NTRS1995

Evolution of Photon and Particle Spectra in Compact, Luminous Objects

Physical conditions in the radiating plasma in the cores of radio-strong quasars and active galactic nuclei cannot be derived from observations until the effects of relativistic aberration are understood. This requires determining both the bulk flow speeds and any wave or signal speed in the parsec-scale nuclear jets. In this project we studied several aspects of such waves. We considered constraints on jet deceleration by mass pickup, and found that bolometric luminosities of the active nuclei cannot constrain core jet speeds usefully. We also simulated observations of ballistic, helical trajectories and helical waves moving directly outwards along the jet. We found that ballistic trajectories are not allowed by the data; the helical features seen are very likely to be helical waves. We believe these are waves propagating in the jet plasma. To this end, we studied waves propagating in relativistic pair plasma jets. In particular, we undertook a program whose goal was to determine the nature of waves which can propagate in relativistic pair plasmas, and how such waves propagating in streaming jet plasma would be observed by an external observer. We developed the possibility of using pulsars as test cases for our models; this takes advantage of new technology in pulsar observations, and the similarity of the physical conditions in the pulsar magnetosphere to the dense, relativistic pair plasmas which exist in radio-strong quasars.

Eilek, Jean A.↗
NASA NTRS2000

Cross-Linking Studies of Lysozyme Nucleation

Tetragonal chicken egg white crystals consist of 4(sub 3) helices running in alternating directions, the helix rows having a two fold symmetry with each other. The unit cell consists of one complete tetrameric turn from each of two adjacent helices (an octamer). PBC analysis indicates that the helix intermolecular bonds are the strongest in the crystal, therefore likely formed first. AFM analysis of the (110) surface shows only complete helices, no half steps or bisected helices being found, while AFM line scans to measure the growth step increments show that they are multiples of the 4(sub 3) helix tetramer dimensions. This supports our thesis that the growth units are in fact multiples of the four molecule 4(sub 3) helix unit, the "average" growth unit size for the (110) face being an octamer (two turns about the helix) and the (101) growth unit averaging about the size of a hexamer. In an effort to better understand the species involved in the crystal nucleation and growth process, we have initiated an experimental program to study the species formed in solution compared to what is found in the crystal through covalent cross-linking studies. These experiments use the heterobifunctional cross-linking agent aminoethyl-4-azidonitroanaline (AEANA). An aliphatic amine at one end is covalently attached to the protein by a carbodiimide-mediated reaction, and a photo reactive group at the other can be used to initiate crosslinking. Modifications to the parent structure can be used to alter the distance between the two reactive groups and thus the cross-linking agents "reach". In practice, the cross-linking agent is first coupled to the asp101 side chain through the amine group. Asp101 lies within the active site cleft, and previous work with fluorescent probes had shown that derivatives at this site still crystallize in the tetragonal space group. This was also found to be the case with the AEANA derivative, which gave red tetragonal crystals. The protein now has a reactive group that can be photoactivated at a specific point in the nucleation or crystal growth process to "capture" protein molecules bound within reach of the crosslinking agent. If those bound protein molecules have a defined geometric relationship with the capturing molecule, such as would be found in a crystal, then the photoreacted cross-linking site should be consistent. Random protein interactions, typical of an amorphous precipitate or interaction, would show a random cross-linking reaction. The results of these and other experiments will be presented.

Forsythe, Elizabeth↗
NASA NTRS1998

Shear-Sensitive Liquid Crystal Coating Method: Surface-Inclination Effects on Shear Vector Measurements

The shear-sensitive liquid crystal coating (SSLCC) method is an image-based technique for both visualizing dynamic surface-flow phenomena, such as transition and separation, and for measuring the continuous shear-stress vector distribution acting on an aerodynamic surface. Under proper lighting and viewing conditions (discussed below), the coating changes color in response to an applied aerodynamic shear. This color-change response is continuous and reversible, with a response time of milliseconds, and is a function of both the shear magnitude and the shear vector orientation relative to the observer. The liquid crystal phase of matter is a weakly-ordered, viscous, non-Newtonian fluid state that exists between the nonuniform liquid phase and the ordered solid phase of certain organic compounds. Cholesteric liquid crystal compounds possess a helical molecular arrangement that selectively scatters white light, incident along the helical axis, as a three-dimensional spectrum. This property is linked to the helical pitch length, which is within the range of wavelengths in the visible spectrum. The pitch length, and hence the wavelength of the scattered light, is influenced by shear stress normal to the helical axis. This unique optical property produces a measurable color change in response to an applied shearing force. The full-surface shear stress vector measurement method, developed at NASA-Ames, is schematically illustrated. As with the visualization method, the coated test surface is illuminated from the normal direction with white light and the camera is positioned at an above-plane view angle of approximately 30 deg. Experiments have been initiated at NASA Ames to begin the process of quantifying surface-inclination (surface-curvature) effects on shear vector measurement accuracy. In preliminary experiments, surface-inclination angles theta(sub x), theta(sub y) of 0, +/-5, +/-10, and +/-15 deg were employed. In this arrangement, white-light illumination was positioned normal to the untilted test surface, and the camera above-plane view angle was set at 30 deg relative to the untilted test surface. As can be seen, vector-aligned lambda(sub d) values showed no dependence on theta(sub x) or theta(sub y) for absolute values of these tilt angles is less than or equal to 15 deg. Acquisition and analyses of full-surface color images are presently underway to definitively document the insensitivity limits of the shear vector measurement methodology to surface-slope variations.

Reda, Daniel C.↗
NASA NTRS2002

Protein Solvation in Membranes and at Water-Membrane Interfaces

Different salvation properties of water and membranes mediate a host of biologically important processes, such as folding, insertion into a lipid bilayer, associations and functions of membrane proteins. These processes will be discussed in several examples involving synthetic and natural peptides. In particular, a mechanism by which a helical peptide becomes inserted into a model membrane will be described. Further, the molecular mechanism of recognition and association of protein helical segments in membranes will be discussed. These processes are crucial for proper functioning of a cell. A membrane-spanning domain of glycophorin A, which exists as a helical dimer, serves as the model system. For this system, the free energy of dissociation of the helices is being determined for both the wild type and a mutant, in which dimerization is disrupted.

Pohorille, Andrew↗
NASA NTRS1999

Differential expression of human lysyl hydroxylase genes, lysine hydroxylation, and cross-linking of type I collagen during osteoblastic differentiation in vitro

The pattern of lysyl hydroxylation in the nontriple helical domains of collagen is critical in determining the cross-linking pathways that are tissue specific. We hypothesized that the tissue specificity of type I collagen cross-linking is, in part, due to the differential expression of lysyl hydroxylase genes (Procollagen-lysine,2-oxyglutarate,5-dioxygenase 1, 2, and 3 [PLOD1, PLOD2, and PLOD3]). In this study, we have examined the expression patterns of these three genes during the course of in vitro differentiation of human osteoprogenitor cells (bone marrow stromal cells [BMSCs]) and normal skin fibroblasts (NSFs). In addition, using the medium and cell layer/matrix fractions in these cultures, lysine hydroxylation of type I collagen alpha chains and collagen cross-linking chemistries have been characterized. High levels of PLOD1 and PLOD3 genes were expressed in both BMSCs and NSFs, and the expression levels did not change in the course of differentiation. In contrast to the PLOD1 and PLOD3 genes, both cell types showed low PLOD2 gene expression in undifferentiated and early differentiated conditions. However, fully differentiated BMSCs, but not NSFs, exhibited a significantly elevated level (6-fold increase) of PLOD2 mRNA. This increase coincided with the onset of matrix mineralization and with the increase in lysyl hydroxylation in the nontriple helical domains of alpha chains of type I collagen molecule. Furthermore, the collagen cross-links that are derived from the nontriple helical hydroxylysine-aldehyde were found only in fully differentiated BMSC cultures. The data suggests that PLOD2 expression is associated with lysine hydroxylation in the nontriple helical domains of collagen and, thus, could be partially responsible for the tissue-specific collagen cross-linking pattern.

NASA Discipline Musculoskeletal↗
NASA NTRS2001

Accurate Time-Dependent Traveling-Wave Tube Model Developed for Computational Bit-Error-Rate Testing

The phenomenal growth of the satellite communications industry has created a large demand for traveling-wave tubes (TWT's) operating with unprecedented specifications requiring the design and production of many novel devices in record time. To achieve this, the TWT industry heavily relies on computational modeling. However, the TWT industry's computational modeling capabilities need to be improved because there are often discrepancies between measured TWT data and that predicted by conventional two-dimensional helical TWT interaction codes. This limits the analysis and design of novel devices or TWT's with parameters differing from what is conventionally manufactured. In addition, the inaccuracy of current computational tools limits achievable TWT performance because optimized designs require highly accurate models. To address these concerns, a fully three-dimensional, time-dependent, helical TWT interaction model was developed using the electromagnetic particle-in-cell code MAFIA (Solution of MAxwell's equations by the Finite-Integration-Algorithm). The model includes a short section of helical slow-wave circuit with excitation fed by radiofrequency input/output couplers, and an electron beam contained by periodic permanent magnet focusing. A cutaway view of several turns of the three-dimensional helical slow-wave circuit with input/output couplers is shown. This has been shown to be more accurate than conventionally used two-dimensional models. The growth of the communications industry has also imposed a demand for increased data rates for the transmission of large volumes of data. To achieve increased data rates, complex modulation and multiple access techniques are employed requiring minimum distortion of the signal as it is passed through the TWT. Thus, intersymbol interference (ISI) becomes a major consideration, as well as suspected causes such as reflections within the TWT. To experimentally investigate effects of the physical TWT on ISI would be prohibitively expensive, as it would require manufacturing numerous amplifiers, in addition to acquiring the required digital hardware. As an alternative, the time-domain TWT interaction model developed here provides the capability to establish a computational test bench where ISI or bit error rate can be simulated as a function of TWT operating parameters and component geometries. Intermodulation products, harmonic generation, and backward waves can also be monitored with the model for similar correlations. The advancements in computational capabilities and corresponding potential improvements in TWT performance may prove to be the enabling technologies for realizing unprecedented data rates for near real time transmission of the increasingly larger volumes of data demanded by planned commercial and Government satellite communications applications. This work is in support of the Cross Enterprise Technology Development Program in Headquarters' Advanced Technology & Mission Studies Division and the Air Force Office of Scientific Research Small Business Technology Transfer programs.

Kory, Carol L.↗