Simulation of polymeric translocation

DNA是一种很长的分子，由一系列称为碱基对的重复单元组成。每个生物体的DNA都有自己独特的碱基对序列，包含该生物体的所有遗传信息;因此，它有时被称为“生命蓝图”。目前用于DNA测序的方法是缓慢且非常昂贵的。快速而廉价的测序方法将对生物医学研究产生重大影响，例如，通过观察和识别引起耐药性的基因突变。一种被提议的替代方法被称为“纳米孔测序”，其中DNA片段穿过屏障中的纳米大小的孔，并且通过监测单元通过时的电信号来读取每个序列单元的身份。一些障碍阻碍了这种技术的发展。例如，使用当前的实验方法，易位太快且不受控制。深入了解易位的基本物理学-DNA通过孔的运输-可以帮助克服这些问题，并指导这种技术的发展。 我将使用计算机模拟来研究聚合物（如DNA）通过纳米孔移位的物理学。仿真是在计算机上对模型系统进行的虚拟实验。模拟用于理解实验观察的意义，并测试理论模型中使用的简化假设。我的研究将解决以下问题：（1）如何调整纳米孔的性质和系统的其他特征，以提供缓慢和受控的移位过程，这是纳米孔测序的要求？(2)使用简单的DNA模型来测量易位“屏障”的模拟是否可以用于理解易位动力学的理论？

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?