Precision Nanotech: The Next Generation of Nanoengineering and Nanomaterials
Multi-scale Computational Methods to SimulateNovel DNA Sequencing Techniques
Alexandre Reily Rocha
Instituto de Física Teórica, Universidade Estadual Paulista (UNESP),
São Paulo, SP
The quest for rapid whole-genome sequencing using new inexpensive techniques is at the forefront of scientific research as we aim to reliably determine genetic predispositions to diseases and gain a deep understanding of our genetic code . Unfortunately, currently available techniques are unlikely to reach the low cost per genome required for this procedure to become widely available in preventive healthcare .
Third-generation devices, in particular, sequencing with nanopores [3,4], is widely regarded as the most promising approach to enable inexpensive whole-genome sequencing and provide orders of magnitude longer base read-lengths. The fabrication of solid-state nanopores along with their envisioned application for rapid whole-genome sequencing is becoming increasingly sophisticated. However, many extremely challenging questions remain unanswered, especially how to achieve single-base resolution during polynucleotide translocation through the nanopore. One proposal is to use tunneling current across the membrane containing the nanopore and use the different electronic transport signals as a signature of the electronic structure of the different nucleotides .
From the theoretical point of view this is a challenging, yet exciting task. On the one hand one must simulate the dynamics of DNA as it passes through a nanopore. The molecule is surrounded by a physiological solution. At the same electrons must be explicitly tread as one wishes to calculate the current passing through the device. In this talk I will discuss recent progress in our group towards completely and realistically simulating a nanopore-based sequencing device . In order to do this, I’ll demonstrate how we combine quantum and classical methodologies in order to address the electronic conductance and the possibility of using graphene-based devices for single-shot DNA sequencing.
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