PyLink: a PyMOL plugin to identify links

2019 ◽  
Vol 35 (17) ◽  
pp. 3166-3168 ◽  
Author(s):  
Aleksandra M Gierut ◽  
Pawel Dabrowski-Tumanski ◽  
Wanda Niemyska ◽  
Kenneth C Millett ◽  
Joanna I Sulkowska
Keyword(s):  
Mechanical Properties ◽  
Disulfide Bonds ◽  
Topological Analysis ◽  
Topological Characterization ◽  
Closed Loops ◽  
Ion Interactions ◽  
Pharmaceutical Applications ◽  
Exceptional Stability ◽  
Pymol Plugin

Abstract Summary Links are generalization of knots, that consist of several components. They appear in proteins, peptides and other biopolymers with disulfide bonds or ions interactions giving rise to the exceptional stability. Moreover because of this stability such biopolymers are the target of commercial and medical use (including anti-bacterial and insecticidal activity). Therefore, topological characterization of such biopolymers, not only provides explanation of their thermodynamical or mechanical properties, but paves the way to design templates in pharmaceutical applications. However, distinction between links and trivial topology is not an easy task. Here, we present PyLink—a PyMOL plugin suited to identify three types of links and perform comprehensive topological analysis of proteins rich in disulfide or ion bonds. PyLink can scan for the links automatically, or the user may specify their own components, including closed loops with several bridges and ion interactions. This creates the possibility of designing new biopolymers with desired properties. Availability and implementation The PyLink plugin, manual and tutorial videos are available at http://pylink.cent.uw.edu.pl.

Topological characterization of deterministic chaos: enforcing orientation preservation

2007 ◽  
Vol 366 (1865) ◽  
pp. 559-567 ◽  
Author(s):  
Marc Lefranc ◽  
Pierre-Emmanuel Morant ◽  
Michel Nizette
Keyword(s):  
Periodic Orbits ◽  
Topological Analysis ◽  
Three Dimensional ◽  
Deterministic Chaos ◽  
Three Dimensions ◽  
Unstable Periodic Orbits ◽  
Topological Characterization ◽  
Triangulated Surfaces ◽  
Theoretic Characterization

The determinism principle, which states that dynamical state completely determines future time evolution, is a keystone of nonlinear dynamics and chaos theory. Since it precludes that two state space trajectories intersect, it is a core ingredient of a topological analysis of chaos based on a knot-theoretic characterization of unstable periodic orbits embedded in a strange attractor. However, knot theory can be applied only to three-dimensional systems. Still, determinism applies in any dimension. We propose an alternative framework in which this principle is enforced by constructing an orientation-preserving dynamics on triangulated surfaces and find that in three dimensions our approach numerically predicts the correct topological entropies for periodic orbits of the horseshoe map.

A Topological Characterization of Conjugate Nets

1977 ◽  
Vol 29 (4) ◽  
pp. 707-721
Author(s):  
Paul A. Vincent
Keyword(s):  
Level Sets ◽  
Harmonic Functions ◽  
Function Theory ◽  
Topological Analysis ◽  
Topological Characterization ◽  
Families Of Curves ◽  
Open Maps

One aspect of topological analysis that authors, such as G. T. Whyburn and Marston Morse, have pointed to ([16; 6] for instance) as being fundamental in the development of function theory is the topological study of the level sets of analytic and harmonic functions or of their topological analogues, light open maps and pseudo-harmonic functions. The first step in this direction seems to have been made by H. Whitney [14] when he studied families of curves, given abstractly using a condition of regularity.

Microstructural and fractographic characterization of B4C-Al cermets tested under dynamic and static loading

1989 ◽  
Vol 47 ◽  
pp. 562-563
Author(s):  
Gyeung Ho Kim ◽  
Mehmet Sarikaya ◽  
D. L. Milius ◽  
I. A. Aksay
Keyword(s):  
Thin Film ◽  
Mechanical Properties ◽  
Fracture Toughness ◽  
Static Loading ◽  
Carbon Deposition ◽  
Full Density ◽  
Unique Combination ◽  
Strong Component ◽  
Reaction Products

Cermets are designed to optimize the mechanical properties of ceramics (hard and strong component) and metals (ductile and tough component) into one system. However, the processing of such systems is a problem in obtaining fully dense composite without deleterious reaction products. In the lightweight (2.65 g/cc) B4C-Al cermet, many of the processing problems have been circumvented. It is now possible to process fully dense B4C-Al cermet with tailored microstructures and achieve unique combination of mechanical properties (fracture strength of over 600 MPa and fracture toughness of 12 MPa-m1/2). In this paper, microstructure and fractography of B4C-Al cermets, tested under dynamic and static loading conditions, are described.The cermet is prepared by infiltration of Al at 1150°C into partially sintered B4C compact under vacuum to full density. Fracture surface replicas were prepared by using cellulose acetate and thin-film carbon deposition. Samples were observed with a Philips 3000 at 100 kV.

Characterization of interfaces in CVD-coated nicalon fiber-reinforced SiC

1989 ◽  
Vol 47 ◽  
pp. 556-557
Author(s):  
K.L. More ◽  
R.A. Lowden
Keyword(s):  
Mechanical Properties ◽  
Fracture Toughness ◽  
Chemical Vapor ◽  
Chemical Vapor Infiltration ◽  
Frictional Stress ◽  
Fiber Reinforced ◽  
Pull Out ◽  
Carbon Coated ◽  
Fiber Matrix

The mechanical properties of fiber-reinforced composites are directly related to the nature of the fiber-matrix bond. Fracture toughness is improved when debonding, crack deflection, and fiber pull-out occur which in turn depend on a weak interfacial bond. The interfacial characteristics of fiber-reinforced ceramics can be altered by applying thin coatings to the fibers prior to composite fabrication. In a previous study, Lowden and co-workers coated Nicalon fibers (Nippon Carbon Company) with silicon and carbon prior to chemical vapor infiltration with SiC and determined the influence of interfacial frictional stress on fracture phenomena. They found that the silicon-coated Nicalon fiber-reinforced SiC had low flexure strengths and brittle fracture whereas the composites containing carbon coated fibers exhibited improved strength and fracture toughness. In this study, coatings of boron or BN were applied to Nicalon fibers via chemical vapor deposition (CVD) and the fibers were subsequently incorporated in a SiC matrix. The fiber-matrix interfaces were characterized using transmission and scanning electron microscopy (TEM and SEM). Mechanical properties were determined and compared to those obtained for uncoated Nicalon fiber-reinforced SiC.

PREPARATION AND CHARACTERIZATION OF REPROCESSED COMPOSITES OF POLYPROPYLENE REINFORCED BY WOOD FIBERS: PHYSICAL AND MECHANICAL PROPERTIES

2017 ◽  
Author(s):  
Thais Helena Sydenstricker Flores-Sahagun ◽  
Kelly Priscila Agapito ◽  
ROSA MARIA JIMENEZ AMEZCUA ◽  
Felipe Jedyn
Keyword(s):  
Mechanical Properties ◽  
Physical And Mechanical Properties ◽  
Wood Fibers

Emerging Techniques for the Characterization of Nano-Mechanical Properties of Integrated Circuit Components

2008 ◽  
Author(s):  
Nicholas Randall ◽  
Rahul Premachandran Nair
Keyword(s):  
Mechanical Properties ◽  
Quality Control ◽  
Integrated Circuits ◽  
Integrated Circuit ◽  
Manufacturing Process ◽  
Solder Bumps ◽  
Initial Work ◽  
Circuit Components ◽  
Materials Used

Abstract With the growing complexity of integrated circuits (IC) comes the issue of quality control during the manufacturing process. In order to avoid late realization of design flaws which could be very expensive, the characterization of the mechanical properties of the IC components needs to be carried out in a more efficient and standardized manner. The effects of changes in the manufacturing process and materials used on the functioning and reliability of the final device also need to be addressed. Initial work on accurately determining several key mechanical properties of bonding pads, solder bumps and coatings using a combination of different methods and equipment has been summarized.

Fabrication and Characterization of Biocomposite Using Grewia Optiva Fibre (i.e. Bhimal) Reinforced Polyvinyl Alcohol (PVA)

2015 ◽  
Vol 1105 ◽  
pp. 51-55 ◽  
Author(s):  
K.M. Gupta ◽  
Kishor Kalauni
Keyword(s):  
Mechanical Properties ◽  
Tensile Strength ◽  
Natural Fibre ◽  
Fabrication Method ◽  
View Point ◽  
Engineering Material ◽  
Fibre Composites ◽  
Grewia Optiva ◽  
Fabrication And Characterization

Bhimal fibres are quite a newer kind of bio-degradable fibres. They have never been heard before in literatures from the view point of their utility as engineering material. These fibres have been utilized for investigation of their properties. Characterization of this fibre is essential to determine its properties for further use as reinforcing fibre in polymeric, bio-degradable and other kinds of matrix. With this objective, the fabrication method and other mechanical properties of Bhimal-reinforced-PVA biocomposite have been discussed. The stress-strain curves and load-deflection characteristics are obtained. The tensile, compressive, flexure and impact strengths have been calculated. The results are shown in tables and graphs. The results obtained are compared with other existing natural fibre biocomposites. From the observations, it has been concluded that the tensile strength of Bhimal-reinforced-PVA biocomposite is higher than other natural fibre composites. Hence these can be used as reinforcement to produce much lighter weight biocomposites.

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