Paper Citing NAMD - Abstract
Jenkins, J.; Sengupta, D.; Sundaram, S.
Characterization of a solid state DNA nanopore sequencer using multi-scale (nano-to-device) modeling
COMPUTATIONAL SCIENCE - ICCS 2005, PT 3, 3516:309-316, 2005
Nanobiotechnology is a rapidly advancing frontier of science with great potential for beneficial impact on society. Unfortunately, design of integrated nano-bio systems is a complex, laborious task with large failure rates. Current models describing molecular level behavior are expensive, while device design codes lack the necessary nanophysics. The objective of this work is to demonstrate multiscale, multiphysics modeling of an integrated nanobio device, where nanoscale effects are efficiently integrated with a continuum model. A three-level modeling paradigm was developed for this purpose. The feasibility of this approach is demonstrated by characterizing a nanopore-based DNA sequencing device. In the demonstration calculations, the dependence of the device performance on the nucleotide sequence, pore diameter, and applied voltage was determined. Extension of the approach for describing biomolecular processes in other commercial nanobiosystems is discussed. The main conclusions of the device level simulations are presented along with an overview of future work.
