Simulation of polymeric translocation

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DNA is a very long molecule composed of a sequence of repeating units called base pairs. The DNA of each organism has its own unique base pair sequence, which comprises all of the genetic information for that organism; consequently, it is sometimes called the "blueprint for life". Current methods for sequencing DNA are slow and very expensive. A fast and cheap sequencing method would have a major impact in biomedical research, for example, by observing and identifying the genetic mutations that give rise to drug resistance. One proposed alternative method is called "nanopore sequencing", whereby a DNA fragment is threaded through a nanometre-sized hole in a barrier, and the identity of each sequence unit is read by monitoring an electric signal as the unit passes through. Several obstacles have prevented the development of such a technology. For example, translocation is far too rapid and uncontrolled using current experimental methods. A deep understanding of the underlying physics of translocation - the transport of the DNA through the pore - could help overcome these problems and guide the development of such a technology. I will use computer simulations to study the physics of the translocation of polymers such as DNA through nanopores. A simulation is a virtual experiment on a model system that is performed on a computer. Simulations are used to understand the meaning of experimental observations and test simplifying assumptions used in theoretical models. My research will address the following questions: (1) How can the properties of the nanopore and other features of the system be adjusted to provide for a slow and controlled translocation process, which is a requirement for nanopore sequencing? (2) Can simulations using simple models of DNA to measure the translocation "barrier" be used in theories to understand the dynamics of translocation?