scholarly journals Reversible Interacting-Particle Reaction Dynamics

2018 ◽  
Vol 122 (49) ◽  
pp. 11240-11250 ◽  
Author(s):  
Christoph Fröhner ◽  
Frank Noé
Keyword(s):  
Reaction Dynamics ◽  
Interacting Particle

scholarly journals ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics

2018 ◽  
Author(s):  
Moritz Hoffmann ◽  
Christoph Fröhner ◽  
Frank Noé
Keyword(s):  
Reaction Kinetics ◽  
Reaction Dynamics ◽  
Md Simulations ◽  
Particle Interactions ◽  
Simulation Environment ◽  
Interacting Particles ◽  
Chemical Reactors ◽  
Interacting Particle ◽  
Computational Work ◽  
Crowded Environments

AbstractInteracting-particle reaction dynamics (iPRD) combines the simulation of dynamical trajectories of interacting particles as in molecular dynamics (MD) simulations with reaction kinetics, in which particles appear, disappear, or change their type and interactions based on a set of reaction rules. This combination facilitates the simulation of reaction kinetics in crowded environments, involving complex molecular geometries such as polymers, and employing complex reaction mechanisms such as breaking and fusion of polymers. iPRD simulations are ideal to simulate the detailed spatiotemporal reaction mechanism in complex and dense environments, such as in signalling processes at cellular membranes, or in nano- to microscale chemical reactors. Here we introduce the iPRD software ReaDDy 2, which provides a Python interface in which the simulation environment, particle interactions and reaction rules can be conveniently defined and the simulation can be run, stored and analyzed. A C++ interface is available to enable deeper and more flexible interactions with the framework. The main computational work of ReaDDy 2 is done in hardware-specific simulation kernels. While the version introduced here provides single- and multi-threading CPU kernels, the architecture is ready to implement GPU and multi-node kernels. We demonstrate the efficiency and validity of ReaDDy 2 using several benchmark examples. ReaDDy 2 is available at the https://readdy.github.io/ website.

scholarly journals ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics

2019 ◽  
Vol 15 (2) ◽  
pp. e1006830 ◽  
Author(s):  
Moritz Hoffmann ◽  
Christoph Fröhner ◽  
Frank Noé
Keyword(s):  
Reaction Dynamics ◽  
Software Framework ◽  
Interacting Particle

Reaction Dynamics — Recent Advances

1991 ◽  
Vol 174 (Part_2) ◽  
pp. 225-225
Author(s):  
Wolfgang Schirmer
Keyword(s):  
Reaction Dynamics ◽  
Recent Advances

Femtosecond reaction dynamics of Rydberg states. Methyl iodide

1993 ◽  
Vol 214 (3-4) ◽  
pp. 281-289 ◽  
Author(s):  
M.H.M. Janssen ◽  
M. Dantus ◽  
H. Guo ◽  
A.H. Zewail
Keyword(s):  
Methyl Iodide ◽  
Rydberg States ◽  
Reaction Dynamics
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