SiSyPHE: A Python package for the Simulation of Systems of interacting mean-field Particles with High Efficiency

Diez, Antoine

doi:10.21105/joss.03653

Cited by 4 publications

(2 citation statements)

References 16 publications

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“…The molecular simulation results were confirmed through the mean-field particle simulation of the water system using Python programming language with SiSyPHE library [17]. The algorithm used was self-propelling algorithm which assumed that each particle is moving with the speed as specified in equation ( 1) [18].…”

Section: Methodsmentioning

confidence: 99%

The mechanism of pH recalibration by dissolved oxygen in alkaline modified aquaculture seawater

Anggayasti

Wardana

et al. 2022

EEJET

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The balance of dissolved oxygen and pH levels is paramount in aquaculture, as a media for cultivating aquatic organisms under controlled conditions. An imbalance in both oxygen and pH could severely harm the cultured aquatic organisms. Various strategies are used to prevent hypoxia and maintain the pH level of the culture. Interestingly, hypoxia or deprivation of oxygen supply in aquaculture was often reported to co-occur with the seawater acidification. Despite that, there was no evidence that the O2 level was directly linked to pH changes. Thus, the existing treatment strategies are separated between O2 and pH maintenances, which often inflate cost and cause environmental burden due to the use of synthetic chemicals. This study was conducted to observe the mechanism and effect of the O2 addition to aquaculture seawater in molecular level when the pH value of the water was modified. The understanding of the mechanism may lead to an alternative to the harmful aquaculture treatments. The molecular mechanics analysis was applied to examine the mechanism of pH adjustment in non-aerated and aerated seawater. The results indicated that O2 accelerated the pH recalibration of seawater, particularly in the alkaline modified samples compared to the acid modified samples. Mechanical simulations further showed the repulsion between and O2 causes vibration which shortens OH bond by 17.71 % while elongates O-O bond by 1.00 %. Additionally, the spin coupling between OH- and O2 promotes global energy transfer which stimulates the vibration of the alkaline modified water system. Together, those mechanisms enabled the pH value to return to the baseline. These findings contribute a molecular mechanism view of aquaculture pH maintenance in the presence of O2, as well as revisiting the use of aeration in aquaculture treatment

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Section: Methodsmentioning

confidence: 99%

The mechanism of pH recalibration by dissolved oxygen in alkaline modified aquaculture seawater

Anggayasti

Wardana

et al. 2022

EEJET

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“…Simulating mean-field particle systems is relatively easy though computationally expensive when the number of particles becomes large. In order to simulate the particle system with up to 3.5 millions particles, we rely on the highly-efficient GPU framework introduced in the SiSyPHE library [38] which is based on the KeOps library [13]. The SiSyPHE library is a versatile Python library designed for the simulation of collective dynamics models which already includes classical models such as the Vicsek model.…”

Section: Particle Schemementioning

confidence: 99%

Topological states and continuum model for swarmalators without force reciprocity

Degond¹,

Diez²,

Walczak³

2022

Preprint

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Swarmalators are systems of agents which are both self-propelled particles and oscillators. Each particle is endowed with a phase which modulates its interaction force with the other particles. In return, relative positions modulate phase synchronization between interacting particles. In the present model, there is no force reciprocity: when a particle attracts another one, the latter repels the former. This results in a pursuit behavior. In this paper, we derive a hydrodynamic model of this swarmalator system and show that it has explicit doubly-periodic travelling-wave solutions in two space dimensions. These special solutions enjoy non-trivial topology quantified by the index of the phase vector along a period in either dimension. Stability of these solutions is studied by investigating the conditions for hyperbolicity of the model. Numerical solutions of both the particle and hydrodynamic models are shown. They confirm the consistency of the hydrodynamic model with the particle one for small times or large phase-noise but also reveal the emergence of intriguing patterns in the case of small phase-noise.

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Bulk Topological States in a New Collective Dynamics Model

Degond¹,

Diez²,

Na³

2022

SIAM J. Appl. Dyn. Syst.

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SiSyPHE: A Python package for the Simulation of Systems of interacting mean-field Particles with High Efficiency

Cited by 4 publications

References 16 publications

The mechanism of pH recalibration by dissolved oxygen in alkaline modified aquaculture seawater

The mechanism of pH recalibration by dissolved oxygen in alkaline modified aquaculture seawater

Topological states and continuum model for swarmalators without force reciprocity

Bulk Topological States in a New Collective Dynamics Model

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