scholarly journals Determination of kinetic properties in unimolecular dissociation of complex systems from graph theory based analysis of an ensemble of reactive trajectories

2021 ◽  
Vol 155 (12) ◽  
pp. 124103
Author(s):  
Ariel F. Perez-Mellor ◽  
Riccardo Spezia
Keyword(s):  
Graph Theory ◽  
Complex Systems ◽  
Kinetic Properties ◽  
Unimolecular Dissociation ◽  
Reactive Trajectories

scholarly journals Determination of Kinetic Properties in Unimolecular Dissociation of Complex Systems from Graph-Theory Based Analysis of an Ensemble of Reactive Trajectories.

2021 ◽  
Author(s):  
Ariel F. Perez-Mellor ◽  
Riccardo Spezia
Keyword(s):  
Graph Theory ◽  
Complex Systems ◽  
Kinetic Properties ◽  
Unimolecular Dissociation ◽  
Theoretical Mass ◽  
Reactive Trajectories ◽  
Direct Counting ◽  
Dynamics Simulations ◽  
State Kinetic

<div>We describe and apply a general approach based on graph-theory to obtain kinetic and structural properties from direct dynamics simulations. In particular, we focus on the unimolecular fragmentation of complex systems in which, prior to dissociation, different events can take place, and notably isomerizations and formation of ion-molecule complex.</div><div>3-state and 4-state kinetic models are thus obtained and rate constants for global or specific pathways are obtained from direct counting and flux calculation, both being in agreement.<br />Finally, we show how a theoretical mass spectrum can also be obtained automatically.<br /></div>

scholarly journals Determination of Kinetic Properties in Unimolecular Dissociation of Complex Systems from Graph-Theory Based Analysis of an Ensemble of Reactive Trajectories.

2021 ◽  
Author(s):  
Ariel F. Perez-Mellor ◽  
Riccardo Spezia
Keyword(s):  
Graph Theory ◽  
Complex Systems ◽  
Kinetic Properties ◽  
Unimolecular Dissociation ◽  
Theoretical Mass ◽  
Reactive Trajectories ◽  
Direct Counting ◽  
Dynamics Simulations ◽  
State Kinetic

<div>We describe and apply a general approach based on graph-theory to obtain kinetic and structural properties from direct dynamics simulations. In particular, we focus on the unimolecular fragmentation of complex systems in which, prior to dissociation, different events can take place, and notably isomerizations and formation of ion-molecule complex.</div><div>3-state and 4-state kinetic models are thus obtained and rate constants for global or specific pathways are obtained from direct counting and flux calculation, both being in agreement.<br>Finally, we show how a theoretical mass spectrum can also be obtained automatically.<br></div>

scholarly journals Determination of Kinetic Properties in Unimolecular Dissociation of Complex Systems from Graph-Theory Based Analysis of an Ensemble of Reactive Trajectories.

2021 ◽  
Author(s):  
Ariel F. Perez-Mellor ◽  
Riccardo Spezia
Keyword(s):  
Graph Theory ◽  
Complex Systems ◽  
Kinetic Properties ◽  
Unimolecular Dissociation ◽  
Theoretical Mass ◽  
Reactive Trajectories ◽  
Direct Counting ◽  
Dynamics Simulations ◽  
State Kinetic

<div>We describe and apply a general approach based on graph-theory to obtain kinetic and structural properties from direct dynamics simulations. In particular, we focus on the unimolecular fragmentation of complex systems in which, prior to dissociation, different events can take place, and notably isomerizations and formation of ion-molecule complex.</div><div>3-state and 4-state kinetic models are thus obtained and rate constants for global or specific pathways are obtained from direct counting and flux calculation, both being in agreement.<br>Finally, we show how a theoretical mass spectrum can also be obtained automatically.<br></div>

scholarly journals Gating Competence of Constitutively Open CLC-0 Mutants Revealed by the Interaction with a Small Organic Inhibitor

2003 ◽  
Vol 122 (3) ◽  
pp. 295-306 ◽  
Author(s):  
Sonia Traverso ◽  
Laura Elia ◽  
Michael Pusch
Keyword(s):  
Chloride Channels ◽  
Bound State ◽  
Side Chain ◽  
Pore Channel ◽  
Kinetic Properties ◽  
Wild Type ◽  
High Affinity ◽  
Critical Residue ◽  
Fast Gating

Opening of CLC chloride channels is coupled to the translocation of the permeant anion. From the recent structure determination of bacterial CLC proteins in the closed and open configuration, a glutamate residue was hypothesized to form part of the Cl−-sensitive gate. The negatively charged side-chain of the glutamate was suggested to occlude the permeation pathway in the closed state, while opening of a single protopore of the double-pore channel would reflect mainly a movement of this side-chain toward the extracellular pore vestibule, with little rearrangement of the rest of the channel. Here we show that mutating this critical residue (Glu166) in the prototype Torpedo CLC-0 to alanine, serine, or lysine leads to constitutively open channels, whereas a mutation to aspartate strongly slowed down opening. Furthermore, we investigated the interaction of the small organic channel blocker p-chlorophenoxy-acetic acid (CPA) with the mutants E166A and E166S. Both mutants were strongly inhibited by CPA at negative voltages with a &gt;200-fold larger affinity than for wild-type CLC-0 (apparent KD at −140 mV ∼4 μM). A three-state linear model with an open state, a low-affinity and a high-affinity CPA-bound state can quantitatively describe steady-state and kinetic properties of the CPA block. The parameters of the model and additional mutagenesis suggest that the high-affinity CPA-bound state is similar to the closed configuration of the protopore gate of wild-type CLC-0. In the E166A mutant the glutamate side chain that occludes the permeation pathway is absent. Thus, if gating consists only in movement of this side-chain the mutant E166A should not be able to assume a closed conformation. It may thus be that fast gating in CLC-0 is more complex than anticipated from the bacterial structures.

The 3D graph approach for breakdown voltage calculation in BaTiO3 ceramics

2021 ◽  
pp. 2150103
Author(s):  
Vojislav V. Mitic ◽  
Branislav Randjelovic ◽  
Ivana Ilic ◽  
Srdjan Ribar ◽  
An-Lu Chun ◽  
...  
Keyword(s):  
Graph Theory ◽  
Crystal Structures ◽  
Breakdown Voltage ◽  
Main Idea ◽  
Experimental Results ◽  
Grain Structure ◽  
Mathematical Approach ◽  
Electronic Parameters ◽  
Mathematical Graph

After pioneering attempts for the introduction of graph theory in the field of ceramics and microstructures, where 1D and 2D graphs were used, in this paper we applied 3D graphs for the breakdown voltage calculation in BaTiO3 sample with some predefined constraints. We have described the relations between grains in the sample and established a mathematical approach for the calculation of breakdown voltage using experimental results. As a result, we introduced mapping between the property of sample and grain structure, then between the grain structure and mathematical graph, using various crystal structures. The main idea was to apply 3D graph theory for the distribution of electronic parameters between the neighboring grains. With this study, we successfully confirmed the possibilities for applications of graphs as a tool for the determination of properties even at the intergranular level.

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