Graph theory approach

1983 ◽  
Vol 48 (8) ◽  
pp. 2097-2117 ◽  
Author(s):  
Vladimír Kvasnička
Keyword(s):  
Organic Chemistry ◽  
Computer Simulation ◽  
Graph Theory ◽  
Chemical Reaction ◽  
Molecular System ◽  
Theory Approach ◽  
Molecular Systems

A graph-theory formalism of the organic chemistry is suggested. The molecular system is considered as a multigraph with loops, the vertices are evaluated by their mapping onto the vocabulary of vertex labels (e.g. atomic symbols). A multiedge of multiplicity t corresponds to a t-tuple (single, double, triple, etc) bond. The chemical reaction of molecular systems is treated by the transformation of graphs. The suggested graph-theory approach allows to formalize many notions and concepts that are naturally emerging in the computer simulation of organic chemistry.

Development of the ChIMES Force Field for Reactive Molecular Systems: Carbon Monoxide at Extreme Conditions

2019 ◽  
Author(s):  
Rebecca Lindsey ◽  
Nir Goldman ◽  
Laurence E. Fried ◽  
Sorin Bastea
Keyword(s):  
Carbon Monoxide ◽  
Molecular System ◽  
Interaction Model ◽  
System Size ◽  
Single Atom ◽  
Reactive System ◽  
Extreme Conditions ◽  
Ambient Conditions ◽  
Molecular Systems ◽  
Three Body

<p>The interatomic Chebyshev Interaction Model for Efficient Simulation (ChIMES) is based on linear combinations of Chebyshev polynomials describing explicit two- and three-body interactions. Recently, the ChIMES model has been developed and applied to a molten metallic system of a single atom type (carbon), as well as a non-reactive molecular system of two atom types at ambient conditions (water). Here, we continue application of ChIMES to increasingly complex problems through extension to a reactive system. Specifically, we develop a ChIMES model for carbon monoxide under extreme conditions, with built-in transferability to nearby state points. We demonstrate that the resulting model recovers much of the accuracy of DFT while exhibiting a 10<sup>4</sup>increase in efficiency, linear system size scalability and the ability to overcome the significant system size effects exhibited by DFT.</p>

The initial reaction mechanism and thermal sensitivity of a fluoropolymer-containing energetic molecular system: the coupling effect of interfacial interactions and free radical reactions

CrystEngComm ◽  
2021 ◽  
Vol 23 (16) ◽  
pp. 3006-3014
Author(s):  
Wen Qian
Keyword(s):  
Free Radical ◽  
Coupling Effect ◽  
Molecular System ◽  
Thermal Sensitivity ◽  
Radical Reactions ◽  
Initial Reaction ◽  
Interfacial Interactions ◽  
Free Radical Reactions ◽  
Molecular Systems ◽  
Reactive Molecular Dynamics

A strategy combining classic and reactive molecular dynamics is applied to find the coupling effect of interfacial interactions and free radical reactions during the initial thermal decomposition of fluoropolymer-containing molecular systems.

scholarly journals Vulnerability Assessment of a Large Electrical Grid by New Graph Theory Approach

2018 ◽  
Vol 16 (2) ◽  
pp. 527-535 ◽  
Author(s):  
J. BEYZA ◽  
J. M. Yusta ◽  
G. J. Correa ◽  
H. F. Ruiz
Keyword(s):  
Graph Theory ◽  
Vulnerability Assessment ◽  
Theory Approach ◽  
Electrical Grid

scholarly journals Exploring the full catalytic cycle of rhodium(i)–BINAP-catalysed isomerisation of allylic amines: a graph theory approach for path optimisation

2017 ◽  
Vol 8 (6) ◽  
pp. 4475-4488 ◽  
Author(s):  
Takayoshi Yoshimura ◽  
Satoshi Maeda ◽  
Tetsuya Taketsugu ◽  
Masaya Sawamura ◽  
Keiji Morokuma ◽  
...  
Keyword(s):  
Graph Theory ◽  
Reaction Mechanism ◽  
Catalytic Cycle ◽  
Theory Approach ◽  
Allylic Amines ◽  
Reaction Route ◽  
Reaction Method ◽  
Mapping Strategy ◽  
Global Reaction ◽  
Induced Reaction

The reaction mechanism of the cationic rhodium(i)–BINAP complex catalysed isomerisation of allylic amines was explored using the artificial force induced reaction method with the global reaction route mapping strategy.

scholarly journals Conserving woodland caribou habitat while maintaining timber yield: a graph theory approach

2016 ◽  
Vol 46 (7) ◽  
pp. 914-923 ◽  
Author(s):  
Jonathan L.W. Ruppert ◽  
Marie-Josée Fortin ◽  
Eldon A. Gunn ◽  
David L. Martell
Keyword(s):  
Graph Theory ◽  
Rangifer Tarandus ◽  
High Volume ◽  
Timber Harvesting ◽  
Optimization Approach ◽  
Theory Approach ◽  
Heuristic Procedure ◽  
Woodland Caribou ◽  
Old Growth ◽  
Old Growth Forest

The fragmentation and loss of old-growth forest has led to the decline of many forest-dwelling species that depend on old-growth forest as habitat. Emblematic of this issue in many areas of the managed boreal forest in Canada is the threatened woodland caribou (Rangifer tarandus caribou (Gmelin, 1788)). We develop a methodology to help determine when and how timber can be harvested to best satisfy both industrial timber supply and woodland caribou habitat requirements. To start, we use least-cost paths based on graph theory to determine the configuration of woodland caribou preferred habitat patches. We then developed a heuristic procedure to schedule timber harvesting based on a trade-off between merchantable wood volume and the remaining amount of habitat and its connectivity during a planning cycle. Our heuristic can attain 84% of the potential woodland caribou habitat that would be available in the absence of harvesting at the end of a 100 year planning horizon. Interestingly, this is more than that which is attained by the current plan (50%) and a harvesting plan that targets high volume stands (32%). Our results indicate that our heuristic procedure (i.e., an ecologically tuned optimization approach) may better direct industrial activities to improve old-growth habitat while maintaining specified timber production levels.

scholarly journals Modelling spatial distributions of alpine vegetation: A graph theory approach to delineate ecologically-consistent species assemblages

2015 ◽  
Vol 30 ◽  
pp. 196-202 ◽  
Author(s):  
A. Mikolajczak ◽  
D. Maréchal ◽  
T. Sanz ◽  
M. Isenmann ◽  
V. Thierion ◽  
...  
Keyword(s):  
Graph Theory ◽  
Species Assemblages ◽  
Spatial Distributions ◽  
Theory Approach ◽  
Alpine Vegetation

A graph theory approach to predicting unfolding pathways of proteins

2000 ◽  
Vol 18 (4-5) ◽  
pp. 553
Author(s):  
Leslie A. Kuhn ◽  
Brandon Hespenheide ◽  
Andrew J. Rader ◽  
M.F. Thorpe
Keyword(s):  
Graph Theory ◽  
Theory Approach
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