Effect of solvent gradient inside the entropic trap on polymer migration

An entropy trap model of thermodynamic anomalies for dual-amorphous water undergoing liquid-liquid phase transition

Water displays numerous anomalously thermodynamic behaviors. However, the working principles behind these anomalies are not well understood, and the liquid-liquid phase transition (LLPT) is often regarded as the potential reason. In this study, we developed an entropy trap model to characterize the thermodynamic LLPT in dual-amorphous water, i.e. having both low-density and high-density liquid water. From the Adam-Gibbs model and free-volume theory, thermodynamic behaviors of water have been described using the proposed model, in which the constitutive relationships among density, heat capacity, thermal expansivity and glass transition temperature have been formulated. Moreover, the glass transition and its connection to thermodynamic behaviors were also investigated for dual-amorphous water. Finally, experimental data reported in the literature were used to verify effectiveness of the proposed model. This study is expected to provide a physical insight into the anomalous thermodynamics of dual-amorphous water undergoing the LLPT.

Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges

Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.

Melting of confined DNA: static and dynamic properties

We study dsDNA (double strand DNA) melting in detail within varying strip-like confinement in a two-dimensional lattice model. The interplay between reduced configurational entropy and attractive base-pairing energy results in a non-monotonic melting profile of DNA. Structural transitions associated with confined DNA melting reveal a stretched or extended state for very strong confinement. By using the exact enumeration method, we investigate the emergence of a local denatured zone e.g. bubbles during DNA melting. The survival time of a single bubble within varying strip width is studied from the Fokker-Planck formalism by considering the bubble size as a reaction co-ordinate. We show that a simple lattice model can capture the sequence heterogeneity effect on DNA melting and bubble dynamics within the strip. Different time scales of bubble zipping for different DNA sequences are found, which may have potential applications in denaturation mapping.