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The electric field driven translocation of charged star polymers through a cylindrical nanopore has been studied using dissipative particle dynamics simulations. The critical field strength required to induce translocation depends on both the number of arms and the number of beads per arm. It may therefore be possible to separate star polyelectrolytes of different arm lengths using electric field driven translocation through a nanopore. The average translocation time exhibits nonmonotonic variation with the number of arms for good solvent conditions. During translocation, a star polymer with many arms is stretched along the pore axis to a lesser extent as compared to its linear counterpart. Unlike a linear chain that shows tension propagation with large tensions for bonds about to enter the pore, a star has the tensest bonds closest to the branch point whose connectivity to multiple arms raises difficulty for its entry and passage.

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Microbial communities are complex living systems that populate the planet with diverse functions and are increasingly harnessed for practical human needs. To deepen the fundamental understanding of their organization and functioning as well as to facilitate their engineering for applications, mathematical modeling has played an increasingly important role. Agent-based models represent a class of powerful quantitative frameworks for investigating microbial communities because of their individualistic nature in describing cells, mechanistic characterization of molecular and cellular processes, and intrinsic ability to produce emergent system properties. This review presents a comprehensive overview of recent advances in agent-based modeling of microbial communities. It surveys the state-of-the-art algorithms employed to simulate intracellular biomolecular events, single-cell behaviors, intercellular interactions, and interactions between cells and their environments that collectively serve as the driving forces of community behaviors. It also highlights three lines of applications of agent-based modeling, namely, the elucidation of microbial range expansion and colony ecology, the design of synthetic gene circuits and microbial populations for desired behaviors, and the characterization of biofilm formation and dispersal. The review concludes with a discussion of existing challenges, including the computational cost of the modeling, and potential mitigation strategies.

The flow-induced translocation of star polymers through a cylindrical nanopore has been studied using dissipative particle dynamics (DPD) simulations. The number of arms, f, was varied with the total number of monomers, N, kept constant. The effect of simulating the capture of the polymer into the pore upon the mean translocation time, <τt>, has been investigated by varying the chain’s initial location. The results indicate that the incorporation of the capture process results in a reduction of <τt> by up to 15%. This is because the chain’s initial location affects the extent of its stretching along the flow direction during translocation. <τt> exhibits nonmonotonic variation with f, in agreement with recently reported results for electric field-driven translocation of star polymers. Its value is larger and shows greater variation with f when the solvent quality is better. For the same value of f, the capture occurs faster in a good solvent. In addition, <τt> is greater for a semiflexible chain than its flexible counterpart as the time required for the branch point to enter the nanopore is longer in the former case.

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