Boyan Penkov
Research
Nanopores are single apertures in a nanoscale membrane, enabling spatially localized mass transport in nanofluidic systems. At thermal equilibrium, this transport mechanism is purely diffusive; under external bias, this transport admits an advective electrophoretic (and electro-osmotic) component for charged species in solution, driving them through the aperture under the effect of the electric field. For charged polymers, this process can be understood as one-dimensional evolution down a potential gradient across the pore, with contributions from the field gradient in the pore, the entropic self-energy of the polymer when coiled, and the pore-polymer friction.
The steep field gradient (megavolts per meter) lead to fast polymer translocation times (mega-bases per second), in turn straining signal fidelity. These technical strengths have led to manifold applications in long-read nucleic acid sequencing, and are poised to supplant existing core sequencing facilities with portable, user-focused field sequencing tools. However, these strengths come at the cost of extensive protein and polymer engineering on the nucleic acid strand, and tax the efficacy of atomic-scale control of soft, amino-acid bases systems.
We re-consider this emerging problem purely in terms of a polymer evolving in a potential landscape, and ask if direct (time-domain) manipulations of the shape of this potential can affect a (time-domain) change in the translocation rate. The key enabling technology is the contemporary development of two-dimensional material superlattices, which foster electrode sizes and shapes that surpass the Debye length scales in physiological solution, leading to strong electroneutrality breakdown near the pore, and enabling field-effect control of translocating charges. We have an FEM model of the electrostatics of this system, and use that to drive a Monte-Carlo model of thermalized polymer evolving in time on an arbitrary energy landscape. Experimentally, we have addressed both point-like salts and polymer-like DNA translocating through contacted superlattices, with both quasi-static and time-domain manipulation of DNA translocation, enabled by custom electronics.
Education
B. S. Cornell University
M. S. Columbia University
