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

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.

Reaction Dynamics — Recent Advances

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

A Distributed-Ledger, Edge-Computing Architecture for Automation and Computer Integration in Semiconductor Manufacturing

2020 ◽  
pp. 13-29
Author(s):  
Da-Yin Liao
Keyword(s):  
Semiconductor Manufacturing ◽  
Manufacturing Systems ◽  
Edge Computing ◽  
Legacy Systems ◽  
Software Framework ◽  
Computer Integration ◽  
Computing Architecture ◽  
Disruptive Technologies ◽  
Distributed Ledger ◽  
Operational Structure

Contemporary 300mm semiconductor manufacturing systems have highly automated and digitalized cyber-physical integration. They suffer from the profound problems of integrating large, centralized legacy systems with small islands of automation. With the recent advances in disruptive technologies, semiconductor manufacturing has faced dramatic pressures to reengineer its automation and computer integrated systems. This paper proposes a Distributed-Ledger, Edge-Computing Architecture (DLECA) for automation and computer integration in semiconductor manufacturing. Based on distributed ledger and edge computing technologies, DLECA establishes a decentralized software framework where manufacturing data are stored in distributed ledgers and processed locally by executing smart contracts at the edge nodes. We adopt an important topic of automation and computer integration for semiconductor research &development (R&D) operations as the study vehicle to illustrate the operational structure and functionality, applications, and feasibility of the proposed DLECA software framework.

Hot spot implementation method of three-layer software framework

2009 ◽  
Vol 29 (9) ◽  
pp. 2541-2545
Author(s):  
Wen HAO ◽  
Ling-mei AI ◽  
Ying-hui WANG
Keyword(s):  
Hot Spot ◽  
Software Framework ◽  
Implementation Method
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