scholarly journals Geometric principles in the assembly of α-helical bundles

2013 ◽  
Vol 371 (1993) ◽  
pp. 20120369 ◽  
Author(s):  
J. V. Pratap ◽  
B. F. Luisi ◽  
C. R. Calladine
Keyword(s):  
Computer Program ◽  
Cylindrical Surface ◽  
Molecular Switch ◽  
Coiled Coils ◽  
Hydrophobic Residues ◽  
Parallel Orientation ◽  
Helical Bundles ◽  
The Third ◽  
Hydrophobic Cores ◽  
Geometrical Explanation

α-Helical coiled coils are usually stabilized by hydrophobic interfaces between the two constituent α-helices, in the form of ‘knobs-into-holes’ packing of non-polar residues arranged in repeating heptad patterns. Here we examine the corresponding ‘hydrophobic cores’ that stabilize bundles of four α-helices. In particular, we study three different kinds of bundle, involving four α-helices of identical sequence: two pack in a parallel and one in an anti-parallel orientation. We point out that the simplest way of understanding the packing of these 4-helix bundles is to use Crick's original idea that the helices are held together by ‘hydrophobic stripes’, which are readily visualized on the cylindrical surface lattice of the α-helices; and that the ‘helix-crossing angle’—which determines, in particular, whether supercoiling is left- or right-handed—is fixed by the slope of the lattice lines that contain the hydrophobic residues. In our three examples the constituent α-helices have hydrophobic repeat patterns of 7, 11 and 4 residues, respectively; and we associate the different overall conformations with ‘knobs-into-holes’ packing along the 7-, 11- and 4-start lines, respectively, of the cylindrical surface lattices of the constituent α-helices. For the first two examples, all four interfaces between adjacent helices are geometrically equivalent; but in the third, one of the four interfaces differs significantly from the others. We provide a geometrical explanation for this non-equivalence in terms of two different but equivalent ways of assembling this bundle, which may possibly constitute a bistable molecular ‘switch’ with a coaxial throw of about 12 Å. The geometrical ideas that we deploy in this paper provide the simplest and clearest description of the structure of helical bundles. In an appendix, we describe briefly a computer program that we have devised in order to search for ‘knobs-into-holes’ packing between α-helices in proteins.

Comparative assessment of informational content of the equations of F.P. Hadlock and the computer program of V.N. Demidov in determination of term of gestation and fetal weight in the III trimester of gestation

2017 ◽  
Author(s):  
E.A. Derkach , O.I. Guseva
Keyword(s):  
Computer Program ◽  
High Precision ◽  
Gestational Age ◽  
Computer Programs ◽  
Comparative Assessment ◽  
Fetal Weight ◽  
Informational Content ◽  
Third Trimester ◽  
The Third

Objectives: to compare the accuracy of equations F.P. Hadlock and computer programs by V.N. Demidov in determining gestational age and fetal weight in the third trimester of gestation. Materials: 328 patients in terms 36–42 weeks of gestation are examined. Ultrasonography was performed in 0–5 days prior to childbirth. Results: it is established that the average mistake in determination of term of pregnancy when using the equation of F.P. Hadlock made 12,5 days, the computer program of V.N. Demidov – 4,4 days (distinction 2,8 times). The mistake within 4 days, when using the equation of F.P. Hadlock has met on average in 23,1 % of observations, the computer program of V.N. Demidov — 65,9 % (difference in 2,9 times). The mistake more than 10 days, took place respectively in 51,7 and 8,2 % (distinction by 6,3 times). At a comparative assessment of size of a mistake in determination of fetal mass it is established that when using the equation of F.P. Hadlock it has averaged 281,0 g, at application of the computer program of V.N. Demidov — 182,5 g (distinction of 54 %). The small mistake in the mass of a fetus which isn't exceeding 200 g at application of the equation of F.P. Hadlock has met in 48,1 % of cases and the computer program of V.N. Demidov — 64,0 % (distinction of 33,1 %). The mistake exceeding 500 g has been stated in 18 % (F.P. Hadlock) and 4,3 % (V.N. Demidov) respectively (distinction 4,2 times). Conclusions: the computer program of V.N. Demidov has high precision in determination of term of a gestation and mass of a fetus in the III pregnancy.

Geometrical Characteristics of Fishing Boats Series of ITU

2007 ◽  
Vol 44 (02) ◽  
pp. 125-137
Author(s):  
Muhsin Aydin ◽  
Aydin Salci
Keyword(s):  
Computer Program ◽  
The Body ◽  
Hull Form ◽  
The Third ◽  
Geometrical Characteristics ◽  
Fishing Boat ◽  
Technical University ◽  
Hull Forms

In the present paper, first 13 hull forms of fishing boats with different block coefficients were generated. Later, 26 hull forms of fishing boats with two different ratios of length to beam were generated by utilizing previous hull forms of fishing boats mentioned. In total, 39 fishing boats were generated. This series is called "Fishing Boats Series of ITU" (Istanbul Technical University). In this Series, the forms of the body stations and beams of the boats are the same for equal block coefficient and different lengths. The ratio of the beam of any station at any waterline to the beam of boat, Bz/B varies with respect to block coefficient, CB. These variations have been represented with the third-degree polynomials. Thus, a hull form of the fishing boat in the desired length and block coefficient can be obtained by using these polynomials. For this purpose, a computer program called "Turetme" was developed. Finally, by using this program, three hull forms of fishing boats were obtained and presented here.

scholarly journals Calculating conjugacy classes in Sylow -subgroups of finite Chevalley groups of rank six and seven

2014 ◽  
Vol 17 (1) ◽  
pp. 109-122 ◽  
Author(s):  
Simon M. Goodwin ◽  
Peter Mosch ◽  
Gerhard Röhrle
Keyword(s):  
Computer Program ◽  
Explicit Formula ◽  
Chevalley Group ◽  
Conjugacy Classes ◽  
Chevalley Groups ◽  
Sylow Subgroups ◽  
Finite Chevalley Group ◽  
Integer Coefficients ◽  
The Third

AbstractLet$G(q)$be a finite Chevalley group, where$q$is a power of a good prime$p$, and let$U(q)$be a Sylow$p$-subgroup of$G(q)$. Then a generalized version of a conjecture of Higman asserts that the number$k(U(q))$of conjugacy classes in$U(q)$is given by a polynomial in$q$with integer coefficients. In [S. M. Goodwin and G. Röhrle,J. Algebra321 (2009) 3321–3334], the first and the third authors of the present paper developed an algorithm to calculate the values of$k(U(q))$. By implementing it into a computer program using$\mathsf{GAP}$, they were able to calculate$k(U(q))$for$G$of rank at most five, thereby proving that for these cases$k(U(q))$is given by a polynomial in$q$. In this paper we present some refinements and improvements of the algorithm that allow us to calculate the values of$k(U(q))$for finite Chevalley groups of rank six and seven, except$E_7$. We observe that$k(U(q))$is a polynomial, so that the generalized Higman conjecture holds for these groups. Moreover, if we write$k(U(q))$as a polynomial in$q-1$, then the coefficients are non-negative.Under the assumption that$k(U(q))$is a polynomial in$q-1$, we also give an explicit formula for the coefficients of$k(U(q))$of degrees zero, one and two.

MAGNETO‐TELLURIC SOUNDING THREE‐LAYER INTERPRETATION CURVES

Geophysics ◽  
1961 ◽  
Vol 26 (4) ◽  
pp. 465-473 ◽  
Author(s):  
S. H. Yungul
Keyword(s):  
Computer Program ◽  
Digital Computer ◽  
Apparent Resistivity ◽  
Infinite Medium ◽  
The Third ◽  
Total Range

To interpret the magneto‐telluric sounding data in terms of layering in the subsurface, one needs a catalog of “standard” curves. The purpose of this paper is to present such a catalog for the three‐layer cases. The calculations were done by incorporating the formulas given by Cagniard (1953) into a digital computer program. The catalog consists of 117 apparent‐resistivity‐vs‐period curves representing ten resistivity combinations. In each case the third, semi‐infinite medium represents the “basement” with infinite resistivity. In addition, a set of two‐layer curves for the total range of resistivity combinations is also given. The procedure in using the curves is briefly explained.

Behavior of Finite Journal Bearings Under Dynamic Loading Conditions

1980 ◽  
Vol 102 (3) ◽  
pp. 333-338 ◽  
Author(s):  
G. S. A. Shawki ◽  
M. O. A. Mokhtar ◽  
Z. S. Safar
Keyword(s):  
Boundary Conditions ◽  
Computer Program ◽  
Variational Methods ◽  
Axial Length ◽  
Reynolds Equation ◽  
Journal Bearing ◽  
Journal Bearings ◽  
The Third ◽  
Dynamic Loading Conditions ◽  
Generalized Reynolds Equation

Performance characteristics for a complete journal bearing of finite axial length are obtained analytically using a new set of boundary conditions. The generalized Reynolds equation is transformed, in the present analysis, into three ordinary differential equations, two of which being readily integrable while the third is solved by variational methods. By the aid of a specially devised computer program, the validity of the analysis has been assured when applied to prescribed journal loci including stationary, circular, elliptical, and linear harmonic journal oscillation.

scholarly journals The Amyloid as a Ribbon-Like Micelle in Contrast to Spherical Micelles Represented by Globular Proteins

Molecules ◽  
2019 ◽  
Vol 24 (23) ◽  
pp. 4395 ◽  
Author(s):  
Mateusz Banach ◽  
Leszek Konieczny ◽  
Irena Roterman
Keyword(s):  
Gaussian Distribution ◽  
Amyloid Fibrils ◽  
Data Bank ◽  
Globular Proteins ◽  
Structural Pattern ◽  
Hydrophobic Residues ◽  
Aqueous Solvent ◽  
Conformational Diversity ◽  
Spherical Micelles ◽  
Hydrophobic Cores

Selected amyloid structures available in the Protein Data Bank have been subjected to a comparative analysis. Classification is based on the distribution of hydrophobicity in amyloids that differ with respect to sequence, chain length, the distribution of beta folds, protofibril structure, and the arrangement of protofibrils in each superfibril. The study set includes the following amyloids: Aβ (1–42), which is listed as Aβ (15–40) and carries the D23N mutation, and Aβ (11–42) and Aβ (1–40), both of which carry the E22Δ mutation, tau amyloid, and α-synuclein. Based on the fuzzy oil drop model (FOD), we determined that, despite their conformational diversity, all presented amyloids adopt a similar structural pattern that can be described as a ribbon-like micelle. The same model, when applied to globular proteins, results in structures referred to as “globular micelles,” emerging as a result of interactions between the proteins’ constituent residues and the aqueous solvent. Due to their composition, amyloids are unable to attain entropically favorable globular forms and instead attempt to limit contact between hydrophobic residues and water by producing elongated structures. Such structures typically contain quasi hydrophobic cores that stretch along the fibril’s long axis. Similar properties are commonly found in ribbon-like micelles, with alternating bands of high and low hydrophobicity emerging as the fibrils increase in length. Thus, while globular proteins are generally consistent with a 3D Gaussian distribution of hydrophobicity, the distribution instead conforms to a 2D Gaussian distribution in amyloid fibrils.

On the Burmester Points of a Plane

1961 ◽  
Vol 28 (1) ◽  
pp. 41-49 ◽  
Author(s):  
Ferdinand Freudenstein ◽  
George N. Sandor
Keyword(s):  
Computer Program ◽  
Digital Computer ◽  
Analytical Form ◽  
Parametric Form ◽  
Kinematic Synthesis ◽  
Geometric Properties ◽  
The Third ◽  
Special Cases ◽  
Uniform Manner

The paper is divided into three parts concerned with the Burmester points associated with five distinct positions of a plane. In the first part, “Theory,” an equation is derived for the location of the Burmester points; algebraic and geometric properties of these points are deduced and special cases considered. An automatic digital-computer program is described in the second part, “Computation,” using a parametric form of the equation for the Burmester points. In the third part, “Application,” the analytical form of Burmester theory is applied to the solution of a variety of problems in plane kinematic synthesis in one uniform manner.

scholarly journals AUG-Segmenter: a user-friendly tool for segmentation of long time series

2010 ◽  
Vol 12 (3) ◽  
pp. 318-328 ◽  
Author(s):  
Abdullah Gedikli ◽  
Hafzullah Aksoy ◽  
N. Erdem Unal
Keyword(s):  
Time Series ◽  
Dynamic Programming ◽  
Linear Regression ◽  
Computer Program ◽  
Branch And Bound ◽  
Real World ◽  
The Third ◽  
Time Series Segmentation ◽  
Long Time ◽  
User Friendly

In this study, three algorithms are presented for time series segmentation. The first algorithm is based on the branch-and-bound approach, the second on the dynamic programming while the third is a modified version of the latter into which the remaining cost concept of the former is introduced. A user-friendly computer program called AUG-Segmenter is developed. Segmentation-by-constant and segmentation-by-linear-regression can be performed by the program. The program is tested on real-world time series of thousands of terms and found useful in performing segmentation satisfactorily and fast.

scholarly journals Evaluation of the cutting ability of two reciprocating instruments (WaveOne Gold e W-file)

2021 ◽  
Vol 10 (14) ◽  
pp. e207101421900
Author(s):  
Adolfo de Matos de Carvalho ◽  
Marcely Reis da Silva ◽  
Matheus Almeida Rodrigues ◽  
Edeilton Santana de Oliveira Junior ◽  
Caio Cesar Souza ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Computer Program ◽  
Nickel Titanium ◽  
Endodontic Treatment ◽  
Experimental Conditions ◽  
The Third ◽  
Fundamental Step ◽  
Before And After ◽  
Reciprocating Instruments ◽  
Cutting Capacity

Instrumentation is a fundamental step in endodontic treatment to promote proper cleaning and shaping of the canal. The objective of this study was to compare the cutting capacity of two reciprocal nickel-titanium systems in simulated canal blocks. Sixty acrylic blocks were used, divided into two groups of reciprocal files (WaveOne Gold - WOG and W-File - WF), each with 30 blocks and divided into 3 groups (n=10) representing the first, second and third uses: WOG1, WOG2, WOG3, WF1, WF2, and WF3, respectively. Ink was injected into the simulated channels, which were covered with laminated paper to avoid affecting the instrumentation. For irrigation, 5mL of saline was used at each instrument change. At the end of instrumentation, the blocks were photographed and analyzed in a computer program to compare the results before and after instrumentation. In the statistical analysis, the tests S Shapiro-Wilk, T for independent samples and Mann Whitney were performed. Under the experimental conditions in which this study was conducted, it is concluded that there were no significant differences in apical transport after the third application. However, the instruments of the W-File group had more conservative preparations with a better centralization capacity compared to the instruments of the WaveOne Gold group, which caused preparations with a larger diameter.

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