scholarly journals On Computation and Analysis of Entropy Measures for Crystal Structures

2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
Muhammad Kamran Siddiqui ◽  
Shazia Manzoor ◽  
Sarfraz Ahmad ◽  
Mohammed K. A. Kaabar
Keyword(s):  
Crystal Structures ◽  
Structural Information ◽  
Topological Indices ◽  
Shannon’S Entropy ◽  
Molecular Graphs ◽  
Shannon's Entropy ◽  
Entropy Measures ◽  
Crystallographic Structures ◽  
Molecular Tubes ◽  
And Mathematics

In recent years, the study of topological indices associated to different molecular tubes and structures gained a lot of attention of the researchers—working in Chemistry and Mathematics. These descriptors play an important role in describing different properties associated to the objects of study. Moreover, Shannon’s entropy concept—a slightly different but more effective approach—provides structural information related to the molecular graphs. In this article, we have computed and analyzed different entropy measures associated to different crystallographic structures. In particular, we have worked on the Zagreb entropies, hyper and augmented Zagreb entropies, and forgotten and Balaban entropies for the crystallographic structures of the cuprite Cu 2 O and titanium difluoride TiF 2 .

scholarly journals Some New Bounds of Weighted Graph Entropies with GA and Gaurava Indices Edge Weights

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Tiejun Wu ◽  
Hafiz Mutee Ur Rehman ◽  
Yu-Ming Chu ◽  
Deeba Afzal ◽  
Jianfeng Yu
Keyword(s):  
Structural Information ◽  
Weighted Graph ◽  
Shannon’S Entropy ◽  
Molecular Graphs ◽  
Shannon's Entropy ◽  
Complex Graph

Motivated by the concept of Shannon’s entropy, the degree-dependent weighted graph entropy was defined which is now become a tool for measurement of structural information of complex graph networks. The aim of this paper is to study weighted graph entropy. We used GA and Gaurava indices as edge weights to define weighted graph entropy and establish some bounds for different families of graphs. Moreover, we compute the defined weighted entropies for molecular graphs of some dendrimer structures.

scholarly journals On entropy measures of molecular graphs using topological indices

2020 ◽  
Vol 13 (8) ◽  
pp. 6285-6298 ◽  
Author(s):  
Shazia Manzoor ◽  
Muhammad Kamran Siddiqui ◽  
Sarfraz Ahmad
Keyword(s):  
Topological Indices ◽  
Molecular Graphs ◽  
Entropy Measures

scholarly journals Comparing entropy measures of idea links in design protocols: Linkography entropy measurement and analysis of differently conditioned design sessions

2007 ◽  
Vol 21 (4) ◽  
pp. 367-377 ◽  
Author(s):  
Jeff W.T. Kan ◽  
Zafer Bilda ◽  
John S. Gero
Keyword(s):  
Shannon’S Entropy ◽  
The Other ◽  
Experimental Conditions ◽  
Design Processes ◽  
Shannon's Entropy ◽  
Entropy Measures ◽  
Measurement And Analysis ◽  
Entropy Measurement ◽  
Quantitative Tool

AbstractThis paper explores using Shannon's entropy of information to measure linkographs of 12 design sessions that involved six architects in two different experimental conditions. The aim is to find a quantitative tool to interpret the linkographs. This study examines if the differences in the design processes and the design outcomes can be reflected in the entropic interpretations. The results show that the overall entropy of one design condition is slightly higher than the other. Further, there are indications that the change of entropy might reflect design outcomes.

Crystal structures of Magnaporthe oryzae trehalose-6-phosphate synthase (MoTps1) suggest a model for catalytic process of Tps1

2019 ◽  
Vol 476 (21) ◽  
pp. 3227-3240 ◽  
Author(s):  
Shanshan Wang ◽  
Yanxiang Zhao ◽  
Long Yi ◽  
Minghe Shen ◽  
Chao Wang ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Conformational Changes ◽  
Magnaporthe Oryzae ◽  
Structural Information ◽  
Complex Structure ◽  
Critical Role ◽  
Catalytic Process ◽  
Structural Basis ◽  
Salt Bridges ◽  
Terminal Domain

Trehalose-6-phosphate (T6P) synthase (Tps1) catalyzes the formation of T6P from UDP-glucose (UDPG) (or GDPG, etc.) and glucose-6-phosphate (G6P), and structural basis of this process has not been well studied. MoTps1 (Magnaporthe oryzae Tps1) plays a critical role in carbon and nitrogen metabolism, but its structural information is unknown. Here we present the crystal structures of MoTps1 apo, binary (with UDPG) and ternary (with UDPG/G6P or UDP/T6P) complexes. MoTps1 consists of two modified Rossmann-fold domains and a catalytic center in-between. Unlike Escherichia coli OtsA (EcOtsA, the Tps1 of E. coli), MoTps1 exists as a mixture of monomer, dimer, and oligomer in solution. Inter-chain salt bridges, which are not fully conserved in EcOtsA, play primary roles in MoTps1 oligomerization. Binding of UDPG by MoTps1 C-terminal domain modifies the substrate pocket of MoTps1. In the MoTps1 ternary complex structure, UDP and T6P, the products of UDPG and G6P, are detected, and substantial conformational rearrangements of N-terminal domain, including structural reshuffling (β3–β4 loop to α0 helix) and movement of a ‘shift region' towards the catalytic centre, are observed. These conformational changes render MoTps1 to a ‘closed' state compared with its ‘open' state in apo or UDPG complex structures. By solving the EcOtsA apo structure, we confirmed that similar ligand binding induced conformational changes also exist in EcOtsA, although no structural reshuffling involved. Based on our research and previous studies, we present a model for the catalytic process of Tps1. Our research provides novel information on MoTps1, Tps1 family, and structure-based antifungal drug design.

scholarly journals Topological Indices of Para-line Graphs of V-Phenylenic Nanostructures

2019 ◽  
Vol 17 (1) ◽  
pp. 260-266 ◽  
Author(s):  
Imran Nadeem ◽  
Hani Shaker ◽  
Muhammad Hussain ◽  
Asim Naseem
Keyword(s):  
Chemical Properties ◽  
Topological Indices ◽  
Structural Chemistry ◽  
Line Graphs ◽  
Physical And Chemical Properties ◽  
Graph Invariants ◽  
Molecular Graphs ◽  
Physical And Chemical ◽  
And Chemical Properties

Abstract The degree-based topological indices are numerical graph invariants which are used to correlate the physical and chemical properties of a molecule with its structure. Para-line graphs are used to represent the structures of molecules in another way and these representations are important in structural chemistry. In this article, we study certain well-known degree-based topological indices for the para-line graphs of V-Phenylenic 2D lattice, V-Phenylenic nanotube and nanotorus by using the symmetries of their molecular graphs.

Investigating the dynamic nature of the ABC transporters: ABCB1 and MsbA as examples for the potential synergies of MD theory and EPR applications

2015 ◽  
Vol 43 (5) ◽  
pp. 1023-1032 ◽  
Author(s):  
Thomas Stockner ◽  
Anna Mullen ◽  
Fraser MacMillan
Keyword(s):  
Crystal Structures ◽  
Conformational Changes ◽  
Abc Transporters ◽  
Epr Spectroscopy ◽  
Structural Information ◽  
Dynamic Properties ◽  
Molecular System ◽  
Synergistic Effects ◽  
Md Simulations ◽  
Substrate Spectrum

ABC transporters are primary active transporters found in all kingdoms of life. Human multidrug resistance transporter ABCB1, or P-glycoprotein, has an extremely broad substrate spectrum and confers resistance against chemotherapy drug treatment in cancer cells. The bacterial ABC transporter MsbA is a lipid A flippase and a homolog to the human ABCB1 transporter, with which it partially shares its substrate spectrum. Crystal structures of MsbA and ABCB1 have been solved in multiple conformations, providing a glimpse into the possible conformational changes the transporter could be going through during the transport cycle. Crystal structures are inherently static, while a dynamic picture of the transporter in motion is needed for a complete understanding of transporter function. Molecular dynamics (MD) simulations and electron paramagnetic resonance (EPR) spectroscopy can provide structural information on ABC transporters, but the strength of these two methods lies in the potential to characterise the dynamic regime of these transporters. Information from the two methods is quite complementary. MD simulations provide an all atom dynamic picture of the time evolution of the molecular system, though with a narrow time window. EPR spectroscopy can probe structural, environmental and dynamic properties of the transporter in several time regimes, but only through the attachment sites of an exogenous spin label. In this review the synergistic effects that can be achieved by combining the two methods are highlighted, and a brief methodological background is also presented.

scholarly journals ASSESSMENT OF URBAN SPRAWL USING SHANNON’S ENTROPY AND FRACTAL ANALYSIS: A CASE STUDY OF ATAKUM, ILKADIM AND CANIK (SAMSUN, TURKEY)

2017 ◽  
Vol 25 (3) ◽  
pp. 264-276 ◽  
Author(s):  
Derya OZTURK
Keyword(s):  
Urban Sprawl ◽  
Fractal Analysis ◽  
Urban Form ◽  
Entropy Method ◽  
Shannon’S Entropy ◽  
Analysis Method ◽  
Maximum Likelihood Classification ◽  
Shannon's Entropy ◽  
Box Counting

Urban sprawl is one of the most important problems in urban development due to its negative environmental and societal impacts. Therefore, the spatial pattern of urban growth should be accurately analyzed and well understood for effective urban planning. This paper focuses on urban sprawl analysis in the Atakum, Ilkadim and Canik districts of Samsun, Turkey. In this study, urban sprawl was examined over a period of 24 years using Shannon's entropy and fractal analysis based on remote sensing and Geographic Information System (GIS). The built-up areas in 1989, 2000 and 2013 were extracted from Landsat TM/ETM+/OLI images using the maximum likelihood classification method, and urban form changes in the 1989–2013 period were investigated. The Shannon's entropy method was used to determine the degree of urban sprawl, and a fractal analysis method based on box counting was used to characterize the urban sprawl. The results show that Atakum, Ilkadim and Canik experienced important changes and have considerable sprawl and complex characteristics now. The study also revealed that there is no monotonic relationship between Shannon's entropy and fractal dimension.

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