Helix Parameter Research Articles

Meshing theory of involute worm drive

The subject of this paper is the establishment of a new meshing theory applicable to the involute worm drive. The method is proposed for determining the meshing characteristic parameters of the involute worm drive using the principal frame on the involute helicoid. A rigorous proof is presented to prove that a helicoid with constant helix parameter ground by a planar grinding wheel is an involute helicoid employing the uniqueness theorem for surfaces in differential geometry. The relationship among the helix angle of base circle, normal pressure angle and helix angle for the involute worm is proved. Using the proposed meshing theory, the numerical simulation of the involute worm drive is carried out to investigate the meshing performance of the involute worm drive. The numerical results reflect that the conjugate zone covers almost the entire worm gear tooth surface. The contact frequency is higher on one side of the worm gear tooth surface. The contact stress is higher near the end face of worm gear. An area of poor lubrication exists in the middle of the worm gear tooth surface.

Kinetics of the Conformational Transformation between B- and A-Forms in the Drew–Dickerson Dodecamer

Some DNA sequences in crystals and in complexes with proteins can exist in the forms intermediate between the B- and A-DNA. Based on this, it was implied that the B-to-A transition for any DNA molecule should go through these intermediate forms also in kinetics. More precisely, the helix parameter Slide has to change first, and the molecule should take the E-form. After that, the Roll parameter changes. In the present work, we simulated the kinetics of the B–A transition in the Drew–Dickerson dodecamer, a known B-philic DNA oligomer. We used the “sugar” coarse-grained model that reproduces ribose flexibility, preserves sequence specificity, employs implicit water and explicit ions, and offers the possibility to vary friction. As the control parameter of the transition, we chose the volume available for a counterion and considered the change from a large to a small volume. In the described system, the B-to-A conformational transformation proved to correspond to a first-order phase transition. The molecule behaves like a small cluster in the region of such a transition, jumping between the A- and B-forms in a wide range of available volumes. The viscosity of the solvent does not affect the midpoint of the transition but only the overall mobility of the system. All helix parameters change synchronously on average, we have not observed the sequence “Slide first, Roll later” in kinetics, and the E-DNA is not a necessary step for the transition between the B- and A-forms in the studied system. So, the existence of the intermediate DNA forms requires specific conditions, shifting the common balance of interactions: certain nucleotide sequence in specific solution or/and the interaction with some protein.

Design and Characterization of Magnetically Actuated Helical Swimmers at Submillimeter-scale

Bacteria with helical flagella show an ideal mechanism to swim at low Reynolds number. For application of artificial microswimmers, it is desirable to identify effects of structural and geometrical parameters on the swimming performance. In this study, a double-end helical swimmer is proposed based on the usual single-end helical one to improve the forward-backward motion symmetry. The propulsion model of the artificial helical microswimmer is described. Influences of each helix parameter on the swimming velocity and propulsion efficiency are further analyzed. The optimal design for achieving a maximum propulsion velocity of submillimeter scale swimmers is performed based on some constraints. An experimental setup consisting of three-pair of Helmholtz coils is built for the helical microswimmers. Experiments of microswimmers with several groups of parameters were performed, and the results show the validity of the analysis and design.

Effect of Helix Parameter Modification onFlow Characteristics of CIDI Diesel EngineHelical Intake Port

This project work involves experimental investigation of helical inlet port flow characteristics for cylinder head of Direct Injection (D.I) diesel engine. The average flow coefficient and swirl number is obtained using a paddle wheel test bench. Intake port helix parameters, i.e., distance between peripheral side wall and valve axis ‘Dp’, width of helical section parallel to valve axis ‘W’ and initial width of the helix ‘Wh’ are measured for different flow boxes for selected different bore and stroke engines. These parameters are modified and detailed analysis has been done to establish the effect on swirl number and average flow coefficient. The second part of work focused on the Computation Fluid Dynamics (CFD) to study flow velocity, flow distribution inside cylinder and to analyze effect of helix parameter change. The experimental study of combined effect of helix parameters, ‘W’, ‘Wh’ and ‘Dp’ indicates that this modification can be initiated for improving flow characteristics if change required in average flow coefficient is small as compared to higher amount of change required in swirl number. The CFD analysis with this modification also shows improvement in swirl generation and flow distribution.

Modifying the Yamaguchi Four-Component Decomposition Scattering Powers Using a Stochastic Distance

Model-based decompositions have gained considerable attention after the initial work of Freeman and Durden. This decomposition which assumes the target to be reflection symmetric was later relaxed in the Yamaguchi et al. decomposition with the addition of the helix parameter. Since then many decomposition have been proposed where either the scattering model was modified to fit the data or the coherency matrix representing the second order statistics of the full polarimetric data is rotated to fit the scattering model. In this paper we propose to modify the Yamaguchi four-component decomposition (Y4O) scattering powers using the concept of statistical information theory for matrices. In order to achieve this modification we propose a method to estimate the polarization orientation angle (OA) from full-polarimetric SAR images using the Hellinger distance. In this method, the OA is estimated by maximizing the Hellinger distance between the un-rotated and the rotated $T_{33}$ and the $T_{22}$ components of the coherency matrix $\mathbf{[T]}$. Then, the powers of the Yamaguchi four-component model-based decomposition (Y4O) are modified using the maximum relative stochastic distance between the $T_{33}$ and the $T_{22}$ components of the coherency matrix at the estimated OA. The results show that the overall double-bounce powers over rotated urban areas have significantly improved with the reduction of volume powers. The percentage of pixels with negative powers have also decreased from the Y4O decomposition. The proposed method is both qualitatively and quantitatively compared with the results obtained from the Y4O and the Y4R decompositions for a Radarsat-2 C-band San-Francisco dataset and an UAVSAR L-band Hayward dataset.

Study on Surface Pressure Distribution Test of Stayed-Cable Using Aerodynamic Measure

Stayed-cable was being considered as an important component of cable-stayed bridge, with characteristics of its low quality, stiffness and damping, among which rain-wind-induced vibration brings the most serious damage in its high amplitude because of its easy conditions to meet. This paper based on the theory of stayed-cable rain-wind-induced vibration, Through comparing different aerodynamic control measures in wind pressure test of ZhiJiang Bridge cable, this paper analyses the variation rules of two and three dimensional cable surface pressure distribution in different aerodynamic measures and cable aerodynamic coefficient in different surface conditions. The results show that: the wind angle influenced surface wind pressure coefficients and aerodynamic coefficient larger, especially between 25 ° and40 °; when the water was between 40 ° and70 °, the aerodynamic coefficient changed obviously, may happen galloping; It recommend that the cable helix parameter K1 was larger and K2 was between 0.01 and 0.03.

Nucleic acid helix structure determination from NMR proton chemical shifts

We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called chemical shift de novo structure derivation protocol employing singular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids.

A simple parameter relating sequences with folding rates of small alpha helical proteins.

It is found that the helix parameter (HP), which favors clustering of non-polar residues, is linearly correlated with the logarithms of rate constants of folding of small two-state alpha-helical proteins. The definition is HP = N(H)(-1) sigma [f(i)+ (f(i-1)+f(i+1))/2], where f(i)=1 or -1, if the i'th residue is hydrophobic or hydrophilic, respectively, N(H) is the number of hydrophobic residues and the summation is taken over the hydrophobic residues.

A novel technique to specifically separate RNAs by Schizophyllan.

Schizophyllan (SPG) is a kind of beta-1,3-glucan which has glucose side chain through a beta-1,6-glycosil bond (Fig. 1). It was found that SPG could form complex with single stranded polynucleotides. SPG complexes with single stranded RNAs that have similar helix parameter to triple stranded SPG thorough hydrogen bonding and hydrophobic interaction. We prepared single stranded SPG appended gel supports. It worked as affinity column for polynucleotides. Poly(C) and poly(A) was retained in the SPG column at low temperature, though poly(G) passed by SPG column without interaction. RNAs trapped in the SPG appended column were released by changing elution buffer under mild condition. This SPG column could use to separation of mRNA which has poly(A) tail. The results obtained led to the conclusion that SPG which has neither cation charge or nucleic base can play as RNA separation material.

Nonlinearly coupled vibrational modes and self-trapped states: Single-vibron-oscillator case with alpha -helix parameters.

Quantum molecular-time-scale generalized-Langevin-equation (MTGLE) theory is applied to calculate spectral linewidths and redshifts of a single vibron oscillator nonlinearly coupled by the Davydov Hamiltonian in the \ensuremath{\alpha}-helix parameter regime to a chain of linearly coupled molecules. Exact values can also be calculated for this problem. The MTGLE theory gives very accurate results for linewidths and less accurate but acceptable results for redshifts over a wide range of temperatures from 10 to 300 K. These results successfully extend previous calculations carried out in the l-alanine parameter regime to the \ensuremath{\alpha}-helix parameter regime with a 30-fold increase in frequency of the vibron oscillator and a 1000-fold increase in the square of the nonlinear coupling constant. In constrast to the l-alanine case, the vibron-oscillator frequency is more than 16 times greater than the largest frequency in the phonon manifold.

Base sequence and helix structure variation in B and A DNA

The observed propeller twist in base-pairs of crystalline double-helical DNA oligomers improves the stacking overlap along each individual helix strand. But, as proposed by Calladine, it also leads to clash or steric hindrance between purines at adjacent base-pairs on opposite strands of the helix. This clash can be relieved by: (1) decreasing the local helix twist angle between base-pairs; (2) opening up the roll angle between base-pairs on the side on which the clash occurs; (3) separating purines by sliding base-pairs along their long axes so that the purines are partially pulled out of the stack (leading to equal but opposite alterations in main-chain torsion angle delta at the two ends of the base-pair); and (4) flattening the propeller twist of the offending base-pairs. Simple sum functions, sigma 1 through sigma 4, are defined, by which the expected local variation in helix twist, base roll angle, torsion angle delta and propeller twist may be calculated from base sequence. All four functions are quite successful in predicting the behavior of B DNA. Only the helix twist and base roll functions are applicable to A DNA, and the helix twist function begins to fail for an A helical RNA/DNA hybrid. Within these limits, the sequence-derived sum functions match the observed helix parameter variation quite closely, with correlation coefficients greater than 0.900 in nearly all cases. Implications of this sequence-derived helix parameter variation for repressor-operator interactions are considered.

Infrared spectra and structure of synthetic polytripeptides

AbstractA number of polytripeptides related to collagen, namely, (Gly‐Pro‐Pro)n, (Gly‐Pro‐Hyp)n, (Gly‐Hyp‐Hyp)n, (Gly‐Pro‐Ala)n, (Gly‐Pro‐Leu)n, (Gly‐Pro‐Gly)n,(Gly‐Ala‐Pro)n, (Gly‐Ala‐Hyp)n, (Ala‐Pro‐Pro)n, and (Ala‐Hyp‐Hyp)n were investigated by the method of ir spectroscopy and hydrogen‐deuterium kinetics. Strength and order of interpeptide hydrogen bonds of the polytripeptides in a triple‐helical conformation were found to depend on the amino acid composition and residue sequence in the triplets. Correlation of X‐ray diffraction and spectroscopic data for (Gly‐Pro‐Hyp)n showed that the increase of the helix parameter in the process of dehydration is accompanied with the weakening of interpeptide hydrogen bonds. Influences of bound water on the length and order of interchain hydrogen bonding was also examined. It was shown that the incorporation of water molecules into the triple helix depends on the amino acid composition and residue sequence. Synthetic models and native collagens were compared.