Computational modeling of nanopore-based devices for single-molecule sensing and sequencing

Nanopore devices are a class of nanofluidic systems which involve the transport of mass and ions through a nanometer sized pore. These systems are widely studied for their attractive applications, ranging from biological analysis (e.g. real-time study of enzyme kinetics, macromolecule detection or sequencing), to blue energy harvesting. Despite their widespread potential applications, the increasing interest of the scientific community and the relevant progress made in the understanding of such systems, the actual design of nanopore based devices remains an open problem. In fact, most theoretical models fail the quantitative prediction of experimental data, since the assumptions on which they are based often fail in the extremely small nanopore region. The coupling of the extreme fluid confinement, geometrical shape and interfacial physico-chemical properties leads to non-trivial electrohydrodynamic transport phenomena in nanofluidic systems, acting at very different time and length scales. In this complex scenario, different computational approaches must be used to get insights into the physical phenomena influencing nanopore experiments. In this thesis, a special focus is put on the nanopore sensing and in particular on the resistive pulse sensing technique, that is the most commonly used approach in this field. Overall, two main important issues are studied: one concerning the sensibility of such sensors, in terms of capability to give different signals for different molecular species; the second accounting for the capture of the analytes of interest. These two issues are approached in this work via Molecular dynamics simulations and continuum models. For what concerns the capture, in Part II is presented a novel mechanisms giving rise to unidirectional electroosmosis flow in uncharged cyclindrical nanopores, independently on the applied voltage polarity. An analytical model is derived and tested against Molecular Dynamics simulations, showing that the phenomenon is robust under variation of the system geometry. The model provides a quantitatively accurate estimation of the electroosmotic velocity that can be used for nanopore system design. Unidirectional electroosmotic flow was found to occur also in a biological pore, the CsgG protein, whose shape resembles the cavitynanopore ideal system. Moreover, the surface pattering needed to elicit this effect is achievable by modern nanofabrication technology. We expect that such phenomenon may find application in nanopore technologies such as alternate current electroosmotic pumps, and nanopore single molecule sensing devices, where calibrating the competition/cooperation between electroosmotis and electrophoresis is crucial to control particle capture, in particular for neutral or weakly charged molecules such as proteins and peptides. For what concerns the distinguishability, in Part III an original computational method is presented that allows the estimation of an effective electrical resistance related to the hindrance of molecules inside a biological nanopores. The method is based on a quasi-1D approximation of the electrical resistance, and uses equilibrium all-atom molecular dynamics simulations to estimate the electrolyte accessible volume through the nanopore in different clogged states. The method is first used to compare the blockage effect of 20 different homopeptides (one for each standard amino acid), inserted into an α-Hemolysin nanopore, Chapter 6. Then, it is also used to assess the distinguishability of three different polysulfides species through a nanopore sensor composed by an α-Hemolysin with a cyclodextrin inserted, which acts as a molecular adapter, Chapter 7. The interaction between three different cyclodextrins with three different polysulfide species is also studied by docking calculations. The works on the distinguishability of homopeptides and the reduced quasi-1D model was peer reviewed and published in the paper "Insights into protein sequencing with an α-Hemolysin nanopore by atomistic simulations", Di Muccio et al., Scientific Reports, 2019 [1]. The method was also employed for supporting the experimental works "Single-molecule dynamics and discrimination between hydrophilic and hydrophobic amino acids in peptides, through controllable, stepwise translocation across nanopores", Asandei, Dragomir, Di Muccio, Chinappi, Park, Luchian, Polymers, 2018 [2] and "Single-sulfur atom discrimination of polysulfides with a protein nanopore for improved batteries", Bétermier, Cressiot, Di Muccio, Jarroux, Bacri, Morozzo Della Rocca, Chinappi, Pelta, Tarascon, Communications Materials, 2020 [3]; Chapter 7 is adapted from this latter work.