Reactive multi-particle collision dynamics with reactive boundary conditions

Sayyidmousavi, Alireza; Rohlf, Katrin

doi:10.1088/1478-3975/aabc35

Cited by 7 publications

(7 citation statements)

References 39 publications

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“…Generally, we can represent space as a continuum (off-lattice) or a discretized lattice model. In the former, each molecule is represented as a point or a hard-body sphere that propagates via Brownian motion in continuous space [7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23] . Bimolecular reaction is often modeled as a collision-based interaction [7,11,12,14,19,21] according to the Smoluchowski model of diffusion-influenced reactions [24,25].…”

Section: Introductionmentioning

confidence: 99%

Reaction-diffusion kinetics on lattice at the microscopic scale

et al. 2018

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Lattice-based stochastic simulators are commonly used to study biological reaction-diffusion processes. Some of these schemes that are based on the reaction-diffusion master equation (RDME), can simulate for extended spatial and temporal scales but cannot directly account for the microscopic effects in the cell such as volume exclusion and diffusion-influenced reactions. Nonetheless, schemes based on the high-resolution microscopic lattice method (MLM) can directly simulate these effects by representing each finite-sized molecule explicitly as a random walker on fine lattice voxels. The theory and consistency of MLM in simulating diffusion-influenced reactions have not been clarified in detail. Here, we examine MLM in solving diffusion-influenced reactions in 3D space by employing the Spatiocyte simulation scheme. Applying the random walk theory, we construct the general theoretical framework underlying the method and obtain analytical expressions for the total rebinding probability and the effective reaction rate. By matching Collins-Kimball and lattice-based rate constants, we obtained the exact expressions to determine the reaction acceptance probability and voxel size. We found that the size of voxel should be about 2% larger than the molecule. The theoretical framework of MLM is validated by numerical simulations, showing good agreement with the off-lattice particle-based method, eGFRD. MLM run time is more than an order of magnitude faster than eGFRD when diffusing macromolecules with typical concentrations observed in the cell. MLM also showed good agreements with eGFRD and mean-field models in case studies of two basic motifs of intracellular signaling, the protein production-degradation process and the dual phosphorylation-dephosphorylation cycle. In addition, when a reaction compartment is populated with volume-excluding obstacles, MLM captures the non-classical reaction kinetics caused by anomalous diffusion of reacting molecules.

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Section: Introductionmentioning

confidence: 99%

Reaction-diffusion kinetics on lattice at the microscopic scale

et al. 2018

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“…For numerical results in this thesis, we have used (RMPC) reactive multiparticle collision dynamics [18], an extension of MPC and a mesoscopic method, that incorporates reaction mechanisms as well. RMPC is a three step method consisting of particle collisions at discrete time steps, reactions, and free-streaming.…”

Section: Particle-based Methods For Rbc Aggregationmentioning

confidence: 99%

“…Random rotation operators in MPC dynamics can be imposed in many different ways. We use the following rule that was presented in [18,17]…”

Section: Implementation Of Random Rotation Operators In Mpc Dynamicsmentioning

confidence: 99%

Stochastic simulations for aggregating systems with non-constant reaction rates

Asghar¹

2023

Preprint

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<p> In this thesis, reactive multi-particle collision dynamics (RMPC) is used for the simulation of aggregation and aggregation-fragmentation systems. RMPC dynamics consists of collisions, reactions, and free streaming. Aggregation and fragmentation is modelled using a reactive mechanism. An infinite system of ODEs called the Smoluchowski differential equations has been used for comparison in the well mixed case. The exact solution for the infinite system is also compared with a finite system RK4 solution that is more appropriate for finite system RMPC simulations. The maximum cluster size is taken to be five, and the domain for stochastic simulations is cubic with periodic boundary conditions. Constant, additive, and multiplicative rates are discussed, and the affects of variations in aggregation and break-up rates are observed. Non-zero, monomer-only initial conditions are used, and the solution for aggregation is obtained with a monomer only initial-concentration equal to 1, as well as b, where b is a constant. The solution for aggregation and break-up is calculated using a monomer-only initial concentration equal to b. The RMPC simulations showed that the RMPC results had a good agreement with the finite-system RK4 solution specially for smaller particle sizes. There was stochastic noise in the RMPC results for all cases that became more pronounced with increase in break-up rate. The novelty of this work consists of RMPC simulation results for additive and multiplicative rates, which has not been simulated using RMPC before. For the system size considered in this work, stochastic effects can be further extended for larger cluster sizes, and to analyse different choices for aggregation and break-up rates. </p>

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“…Most implementations of chemical reactions in SRD are homogeneous reactions 24,25 or surface reactions with neglect of some processes such as adsorption, surface diffusion, or desorption through the use of mean-field rate expressions. 26,27 Models of colloidal particles propelled by chemical reactions with adsorption-desorption kinetics such as diffusiophoretic Janus colloids and bi-particle catalytic reactions have been described before. [28][29][30][31][32][33] However, these works do not describe the detailed kinetics of changing catalyst sites.…”

Section: Introductionmentioning

confidence: 99%

Coupling mesoscale transport to catalytic surface reactions in a hybrid model

Fan

Habibi

Padding³

et al. 2022

The Journal of Chemical Physics

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In heterogeneous catalysis, reactivity and selectivity are not only influenced by chemical processes occurring on catalytic surfaces but also by physical transport phenomena in the bulk fluid and fluid near the reactive surfaces. Because these processes take place at a large range of time and length scales, it is a challenge to model catalytic reactors, especially when dealing with complex surface reactions that cannot be reduced to simple mean-field boundary conditions. As a particle-based mesoscale method, Stochastic Rotation Dynamics (SRD) is well suited for studying problems that include both microscale effects on surfaces and transport phenomena in fluids. In this work, we demonstrate how to simulate heterogeneous catalytic reactors by coupling an SRD fluid with a catalytic surface on which complex surface reactions are explicitly modeled. We provide a theoretical background for modeling different stages of heterogeneous surface reactions. After validating the simulation method for surface reactions with mean-field assumptions, we apply the method to non-mean-field reactions in which surface species interact with each other through a Monte Carlo scheme, leading to island formation on the catalytic surface. We show the potential of the method by simulating a more complex three-step reaction mechanism with reactant dissociation.

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Reactive multi-particle collision dynamics with reactive boundary conditions

Cited by 7 publications

References 39 publications

Reaction-diffusion kinetics on lattice at the microscopic scale

Reaction-diffusion kinetics on lattice at the microscopic scale

Stochastic simulations for aggregating systems with non-constant reaction rates

Coupling mesoscale transport to catalytic surface reactions in a hybrid model

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