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An enhanced understanding about the interactions between nanomaterials and cell membranes may have important implications for biomedical applications. In this work, coarse-grained molecular dynamics simulations of gold nanoparticles interacting with lipid bilayers were performed to evaluate the effect of hydrophobicity, charge density and ligand length on lipid bilayers. The simulations accomplished indicate that hydrophobic and anionic nanoparticles do not exhibit significant interactions and different charge densities may induce pore formation or nanoparticle wrapping, resembling first stages of endocytosis. The suggested interplay between charge density and ligand length has important implications when designing nanoparticles for drug and gene delivery applications. Moreover, control of charge densities may induce internalization of nanoparticles into cells through different mechanisms such as passive translocation, for nanoparticles with low charge density, or endocytosis for higher charge densities, highlighting the role of surface chemistry in nanoparticle-cell interactions.

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A better understanding of the cell-fate transitions that occur in complex cellular ecosystems in normal development and disease could inform cell engineering efforts and lead to improved therapies. However, a major challenge is to simultaneously identify new cell states, and their transitions, to elucidate the gene expression dynamics governing cell-type diversification. Here, we present CellRouter, a multifaceted single-cell analysis platform that identifies complex cell-state transition trajectories by using flow networks to explore the subpopulation structure of multi-dimensional, single-cell omics data. We demonstrate its versatility by applying CellRouter to single-cell RNA sequencing data sets to reconstruct cell-state transition trajectories during hematopoietic stem and progenitor cell (HSPC) differentiation to the erythroid, myeloid and lymphoid lineages, as well as during re-specification of cell identity by cellular reprogramming of monocytes and B-cells to HSPCs. CellRouter opens previously undescribed paths for in-depth characterization of complex cellular ecosystems and establishment of enhanced cell engineering approaches.