Analyte translocation involves three phases: (i) diffusion in the loading solution; (ii) capture by the pore; (iii) threading. The capture process remains poorly characterized because it cannot easily be visualized or inferred from indirect measurements. The capture performance of a device is often described by a capture radius generally defined as the radial distance R * at which diffusion-dominated dynamics cross over to fieldinduced drift. However, this definition is rather ambiguous and the related models are usually over-simplified and studied in the steady-state limit. We investigate different approaches to defining and estimating R * for a charged particle diffusing in a liquid and attracted to the nanopore by the electric field. We present a theoretical analysis of the Péclet number as well as Monte Carlo simulations with different simulation protocols. Our analysis shows that the boundary conditions, pore size and finite experimental times all matter in the interpretation and calculation of R * .

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During embryogenesis, the spherical inner cell mass (ICM) proliferates in the confined environment of a blastocyst. Embryonic stem cells (ESCs) are derived from the ICM, and mimicking embryogenesis in vitro, mouse ESCs (mESCs) are often cultured in hanging droplets. This promotes the formation of a spheroid as the cells sediment and aggregate owing to increased physical confinement and cell-cell interactions. In contrast, mESCs form two-dimensional monolayers on flat substrates and it remains unclear if the difference in organization is owing to a lack of physical confinement or increased cell-substrate versus cell-cell interactions. Employing microfabricated substrates, we demonstrate that a single geometric degree of physical confinement on a surface can also initiate spherogenesis. Experiment and computation reveal that a balance between cell-cell and cell-substrate interactions finely controls the morphology and organization of mESC aggregates. Physical confinement is thus an important regulatory cue in the three-dimensional organization and morphogenesis of developing cells.

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We introduce an efficient KMC algorithm to simulate voltage-driven translocation, as well as a new pulsed-field method to selectively translocate molecules.