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Stochastic Resonance Behavior of DNA Translocation with an Oscillatory Electric Field
bioRxiv - Biophysics Pub Date : 2021-06-22 , DOI: 10.1101/2021.06.21.449299 Ining A. Jou , Rhys A. Duff , Murugappan Muthukumar
bioRxiv - Biophysics Pub Date : 2021-06-22 , DOI: 10.1101/2021.06.21.449299 Ining A. Jou , Rhys A. Duff , Murugappan Muthukumar
Stochastic resonance (SR) describes the synchronization between noise of a system and an applied oscillating field to achieve an optimized response signal. In this work, we use simulations to investigate the phenomenon of SR of a single stranded DNA driven through a nanopore when an oscillating electric field is added. The system is comprised of a MspA protein nanopore embedded in a membrane and different lengths of DNA is driven from one end of the pore to the other via a constant potential difference. We superimposed an oscillating electric field on top of the existing electric field. The source of noise is due to thermal fluctuations, since the system is immersed in solution at room temperature. Here, the signal optimization we seek is the increase in translocation time of DNA through the protein nanopore. Normally, translocation time scales linearly with DNA length and inversely with driving force in a drift dominanted regime. We found a non monotonic dependence of the mean translocation time with the frequency of the oscillating field. This non-monotonic behavior of the translocation time is observed for all lengths of DNA, but SR occurs only for longer DNA. Furthermore, we also see evidence of DNA extension being influenced by the oscillating field while moving through the nanopore.
中文翻译:
振荡电场下 DNA 易位的随机共振行为
随机共振 (SR) 描述了系统噪声与施加的振荡场之间的同步,以实现优化的响应信号。在这项工作中,我们使用模拟来研究添加振荡电场时通过纳米孔驱动的单链 DNA 的 SR 现象。该系统由嵌入膜中的 MspA 蛋白纳米孔组成,不同长度的 DNA 通过恒定电位差从孔的一端驱动到另一端。我们在现有电场的顶部叠加了一个振荡电场。噪声源是由热波动引起的,因为系统在室温下浸入溶液中。在这里,我们寻求的信号优化是增加 DNA 通过蛋白质纳米孔的易位时间。一般,易位时间与 DNA 长度成线性比例,与漂移主导区域的驱动力成反比。我们发现平均易位时间与振荡场频率的非单调依赖性。对于所有长度的 DNA,都可以观察到易位时间的这种非单调行为,但 SR 仅发生在较长的 DNA 上。此外,我们还看到 DNA 延伸在穿过纳米孔时受到振荡场影响的证据。
更新日期:2021-06-25
中文翻译:
振荡电场下 DNA 易位的随机共振行为
随机共振 (SR) 描述了系统噪声与施加的振荡场之间的同步,以实现优化的响应信号。在这项工作中,我们使用模拟来研究添加振荡电场时通过纳米孔驱动的单链 DNA 的 SR 现象。该系统由嵌入膜中的 MspA 蛋白纳米孔组成,不同长度的 DNA 通过恒定电位差从孔的一端驱动到另一端。我们在现有电场的顶部叠加了一个振荡电场。噪声源是由热波动引起的,因为系统在室温下浸入溶液中。在这里,我们寻求的信号优化是增加 DNA 通过蛋白质纳米孔的易位时间。一般,易位时间与 DNA 长度成线性比例,与漂移主导区域的驱动力成反比。我们发现平均易位时间与振荡场频率的非单调依赖性。对于所有长度的 DNA,都可以观察到易位时间的这种非单调行为,但 SR 仅发生在较长的 DNA 上。此外,我们还看到 DNA 延伸在穿过纳米孔时受到振荡场影响的证据。