Coupling of mitochondrial population evolution to microtubule dynamics in fission yeast cells: a kinetic Monte Carlo study

Abstract

Mitochondrial populations in cells are maintained by cycles of fission and fusion events. Perturbation of this balance has been observed in several diseases such as cancer and neurodegeneration. In fission...

Simulation time analysis of kinetic Monte Carlo algorithmic steps for basic radical (de)polymerization kinetics of linear polymers

“…On top of that, they can be combined with phenomenological models for (mass) transport mechanisms, e.g., diffusion or dispersion, to obtain a detailed description of the studied processes, examples being modelling of traffic and pedestrian flow, 25,26 film, drop or crystal growth, [27][28][29][30][31] vapor deposition, 32,33 atom diffusion on surfaces, 34 electronic and electrochemical applications, [35][36][37] adsorption and heterogeneous catalysis, [38][39][40][41] polycondensation of sugars, 42 epidemiology, 43 kinetics of nucleobases, 44 protein aggregation, 45 and biological and biochemical systems. [46][47][48] The field of polymer reaction engineering (PRE), being the application area in the present work, is a fertile ground to apply kMC algorithms as well, as polymerization kinetics are affected by variations in chain length, chemical composition, and branch location, and, hence, the polymeric macroscopic properties are affected by distributed macromolecular features. 15,[49][50][51] The kMC algorithm has been successfully applied, for instance for free radical polymerization (FRP), [52][53][54][55][56] reversible deactivation radical polymerization (RDRP), 57,58 including atom transfer radical polymerization (ATRP), [59][60][61][62] reversible addition-fragment...…”

“…, diffusion or dispersion, to obtain a detailed description of the studied processes, examples being modelling of traffic and pedestrian flow, 25,26 film, drop or crystal growth, 27–31 vapor deposition, 32,33 atom diffusion on surfaces, 34 electronic and electrochemical applications, 35–37 adsorption and heterogeneous catalysis, 38–41 polycondensation of sugars, 42 epidemiology, 43 kinetics of nucleobases, 44 protein aggregation, 45 and biological and biochemical systems. 46–48…”

A Signal‐To‐Noise‐Ratio‐Based Automated Algorithm to accelerate Kinetic Monte Carlo Convergence in Basic Polymerizations

“…Such upgraded population-driven output includes, e.g., microscopic distributed compositional or topological information, which can be linked to macroscopic properties at the application level as relevant for manufacturers and end users. [33][34][35] It is thus not surprising that the kMC method has shown to be relevant to simulate distributed populations, with many examples in several fields such as electronic component design, [36] molecular interface dynamics, [37] heterogeneous catalysis, [38] film growth and crystallization, [39,40] biological population evolution, [41] nucleation kinetics, [42] and particle growth. [43][44][45] An additional field in which the kMC method has demonstrated its capabilities and versatility, and the main focus of the present work, is polymer reaction engineering (PRE).…”