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 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 The Integrated Density of States for an Interacting Multiparticle Homogeneous Model and Applications to the Anderson Model

2009 ◽  
Vol 2009 ◽  
pp. 1-15 ◽  
Author(s):  
Frédéric Klopp ◽  
Heribert Zenk
Keyword(s):  
Density Of States ◽  
Anderson Model ◽  
Homogeneous Model ◽  
Free Particle ◽  
Integrated Density Of States ◽  
Interacting Particles ◽  
Wegner Estimate ◽  
Homogeneous Potential ◽  
Interacting Particle ◽  
Regularity Properties

For a system of interacting particles moving in the background of a “homogeneous” potential, we show that if the single particle Hamiltonian admits a density of states, so does the interacting -particle Hamiltonian. Moreover, this integrated density of states coincides with that of the free particle Hamiltonian. For the interacting -particle Anderson model, we prove regularity properties of the integrated density of states by establishing a Wegner estimate.

Dual role of friction in granular flows: attenuation versus enhancement of instabilities

2013 ◽  
Vol 729 ◽  
pp. 484-495 ◽  
Author(s):  
Peter P. Mitrano ◽  
Steven R. Dahl ◽  
Andrew M. Hilger ◽  
Christopher J. Ewasko ◽  
Christine M. Hrenya
Keyword(s):  
Cooling System ◽  
Translational Motion ◽  
Granular Flows ◽  
Md Simulations ◽  
Particle Interactions ◽  
Frictional Dissipation ◽  
Inelastic Dissipation ◽  
The Stability ◽  
The Impact

AbstractFlow instabilities driven by the dissipative nature of particle–particle interactions have been well documented in granular flows. The bulk of previous studies on such instabilities have considered the impact of inelastic dissipation only and shown that instabilities are enhanced with increased dissipation. The impact of frictional dissipation on the stability of grains in a homogeneous cooling system is studied in this work using molecular dynamics (MD) simulations and kinetic-theory-based predictions. Surprisingly, both MD simulations and theory indicate that high levels of friction actually attenuate instabilities relative to the frictionless case, whereas moderate levels enhance instabilities compared to frictionless systems, as expected. The mechanism responsible for this behaviour is identified as the coupling between rotational and translational motion. These results have implications not only for granular materials, but also more generally to flows with dissipative interactions between constituent particles – cohesive systems with agglomeration, multiphase flows with viscous dissipation, etc.

scholarly journals Scattering properties of two singularly interacting particles on the half-line

2017 ◽  
Vol 29 (10) ◽  
pp. 1750032 ◽  
Author(s):  
Sebastian Egger ◽  
Joachim Kerner
Keyword(s):  
Weak Coupling ◽  
Scattering Amplitude ◽  
Spatial Localization ◽  
Weak Coupling Limit ◽  
Half Line ◽  
Particle Interactions ◽  
Interacting Particles ◽  
Two Body Problem ◽  
Embedded Eigenvalues ◽  
Generalized Eigenfunctions

We analyze scattering in a system of two (distinguishable) particles moving on the half-line [Formula: see text] under the influence of singular two-particle interactions. Most importantly, due to the spatial localization of the interactions, the two-body problem is of a non-separable nature. We will discuss the presence of embedded eigenvalues and using the obtained knowledge about the kernel of the resolvent, we prove a version of the limiting absorption principle. Furthermore, by an appropriate adaptation of the Lippmann–Schwinger approach, we are able to construct generalized eigenfunctions which consequently allow us to establish an explicit expression for the (on-shell) scattering amplitude. An approximation of the scattering amplitude in the weak-coupling limit is also derived.

scholarly journals Synchronic and diachronic identity for elementary particles

2020 ◽  
Vol 10 (3) ◽  
Author(s):  
Tomasz Bigaj
Keyword(s):  
Elementary Particles ◽  
Particle Interactions ◽  
Interacting Particles ◽  
Quantum Particles ◽  
Before And After

Abstract The main focus of this paper is on the notion of transtemporal (diachronic) identity applied to quantum particles. I pose the question of how the symmetrization postulate with respect to instantaneous states of particles of the same type affects the possibility of identifying interacting particles before and after their interaction. The answer to this question turns out to be contingent upon the choice between two available conceptions of synchronic individuation of quantum particles that I call the orthodox and heterodox approaches. I argue that the heterodox approach offers a better explanation of the known experimental facts regarding particle interactions, and I probe deeper the concepts of synchronic and diachronic identity emerging from this approach.

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 Ion-exchange mechanisms and interfacial reaction kinetics during aqueous corrosion of sodium silicate glasses

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Lu Deng ◽  
Katsuaki Miyatani ◽  
Michinori Suehara ◽  
Shin-ichi Amma ◽  
Madoka Ono ◽  
...  
Keyword(s):  
Ion Exchange ◽  
Reaction Kinetics ◽  
Interfacial Reaction ◽  
Md Simulations ◽  
Interfacial Reactions ◽  
Silicate Glasses ◽  
Initial Surface ◽  
Aqueous Corrosion ◽  
Oxygen Tetrahedron ◽  
Property Changes

AbstractThe ion-exchange and associated interfacial reaction mechanisms of silicate glasses are critical in elucidating their aqueous corrosion behaviors, surface modification and property changes, hence have potential impact on both science and technology. This work reports findings of the atomic and nanoscale details of the glass–water interfacial reactions revealed by applying reactive force field (ReaxFF) based molecular dynamics (MD) simulations, from which the key mechanisms of the ion exchange, as well as the kinetics of associated interfacial reactions, are elucidated. It was found that the Na+ and H+ ion exchange can happen between two oxygen ions on a single silicon oxygen tetrahedron or adjacent tetrahedra. In addition, the clustered reaction of two non-bridging oxygens mediated by an adjacent water molecule was also identified. The latter reaction might be the main mechanism of water transport after initial surface reactions that consume the non-bridging oxygen species on the surface. Water molecules thus can play two roles: as an intermediate during the proton transfer processes and as a terminator of the clustered reactions. Statistical analyses were performed to obtain reaction kinetics and the results show that silanol formation is a more favored process than the silanol re-formation within the first 3 ns of interfacial reactions. The results obtained thus shed lights on the complex ion-exchange mechanisms during glass hydration and enable more detailed understanding of the corrosion and glass–water interactions of silicate glasses.

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