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Characterization of a Solid State DNA Nanopore Sequencer using Multi-Scale (Nano-to-Device) Modeling

J.W. Jenkins, D. Sengupta and S. Sundaram
CFD Research Corporation, US

nanopore, DNA sequencing, molecular modeling

The rapid convergence of nanotechnology and biotechnology has generated a need for design tools that can incorporate sufficiently detailed models of the nanoscale molecular phenomena with overarching transport and related effects in microfluidic devices. Currently, no software is available that can perform this task. This void is sought to be filled by our recent efforts, whose innovative aspects include: Ø Development of a novel multi-scale simulation tool for integrated nanosystem design, analysis and optimization Ø Three-tiered modeling approach consisting of (a) molecular models (b) coarse-grained stochastic models and (c) device scale continuum models Ø Development of a unified computing environment that couples stochastic models incorporating molecular behavior with state-of-the-art multi-physics simulation tool. The generalized three-level modeling paradigm under development integrates nanoscale effects of arbitrary biosystems accurately, efficiently and seamlessly using coarse-grained stochastic models carrying molecular information (Figure 1). The first step in the paradigm is to perform molecular simulations to elucidate the essential molecular behavior. Next, stochastic simulation methods, such as the Master Equation, are developed to describe the fast time scale of the molecular system. Finally, the information from the stochastic models is coupled to the continuum CFD model. The approach is demonstrated through a Proof-of-Concept study of a notional nanopore based DNA sequencing device. In nanopore based sequencing, a voltage is applied to a system containing a single nanopore surrounded by DNA in an aqueous ionic solution. The voltage induces the charged DNA to migrate to the nanopore and translocate through it. As the DNA is moving through the nanopore the ionic current is temporarily blocked, providing an electrical signal that depends on the characteristics of the DNA sequence passing through the pore. In the demonstration calculations (summarized in Figure 2), the dependence of the device performance on the nucleotide sequence, pore diameter, and applied voltage will be shown. The molecular modeling consists of a molecular model of two sequences of DNA, along with solid state nanopores of 1.5 and 2.0 nm diameter in a 5.0 nm thick film of silicon dioxide. Molecular simulations provided free energy profiles along the translocation coordinate. These profiles were used to compute the distribution of translocation times and their dependence on voltage. This information was then coupled into the device level calculations to evaluate a proposed ultrahigh throughput DNA sequencing device consisting of 144 patches with 250 nanopores each. The main conclusions of the device level simulations will be presented along with an overview of future work. The end result of this effort will be integral to the rapid development of nanobiosystems including those intended for space exploration and space biology. We have begun work on the development of a hierarchical simulation and modeling tool, which will allow us to develop relationships that describe how molecular characteristics, and fluidics influence the performance of a nanobiosystem. These relationships, and the resulting simulation tool, will aid the design of micro/nanodevices that span a wide spectrum of applications.

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