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.

Self-Assembly of DNA-Grafted Colloids: A Review of Challenges.

DNA-mediated self-assembly of colloids has emerged as a powerful tool to assemble the materials of prescribed structure and properties. The uniqueness of the approach lies in the sequence-specific, thermo-reversible hybridization of the DNA-strands based on Watson-Crick base pairing. Grafting particles with DNA strands, thus, results into building blocks that are fully programmable, and can, in principle, be assembled into any desired structure. There are, however, impediments that hinder the DNA-grafted particles from realizing their full potential, as building blocks, for programmable self-assembly. In this short review, we focus on these challenges and highlight the research around tackling these challenges.

Long-term Retrospective Study based on Implant Success Rate in Patients with Risk Factor: 15-year Follow-up.

AIM: The purpose of this retrospective study is to assess implant success rates with various risk factors. MATERIALS AND METHODS: Two hundred patients with a total of 650 implants were selected. Risk factors, such as smoking, antidepressants, bruxism, diabetes, and bone augmentation procedures were considered, and patients were followed up for a period of 8 to 15 years. RESULTS: Of 650 implants placed, the success rate was 88%, i.e., a total of 572 implants were successful. A total of 78 implants were considered failure; and out of 78, twenty implants were surgically removed. CONCLUSION: Based on this study's results, it is concluded that risk factors, such as smoking, bruxism, diabetes, and bone augmentation play an important role in success rate of dental implants. CLINICAL SIGNIFICANCE: Several factors, such as bruxism, diabetes, and supporting bone can play an important role in dental implant success.

Density-functional theory for fluid-solid and solid-solid phase transitions.

We develop a theory to describe solid-solid phase transitions. The density functional formalism of classical statistical mechanics is used to find an exact expression for the difference in the grand thermodynamic potentials of the two coexisting phases. The expression involves both the symmetry conserving and the symmetry broken parts of the direct pair correlation function. The theory is used to calculate phase diagram of systems of soft spheres interacting via inverse power potentials u(r)=ε(σ/r)^{n}, where parameter n measures softness of the potential. We find that for 1/n<0.154 systems freeze into the face centered cubic (fcc) structure while for 1/n≥0.154 the body-centred-cubic (bcc) structure is preferred. The bcc structure transforms into the fcc structure upon increasing the density. The calculated phase diagram is in good agreement with the one found from molecular simulations.

Fluid-solid transition in simple systems using density functional theory.

A free energy functional for a crystal which contains both the symmetry-conserved and symmetry-broken parts of the direct pair correlation function has been used to investigate the fluid-solid transition in systems interacting via purely repulsive Weeks-Chandler-Anderson Lennard-Jones potential and the full Lennard-Jones potential. The results found for freezing parameters for the fluid-face centred cubic crystal transition are in very good agreement with simulation results. It is shown that although the contribution made by the symmetry broken part to the grand thermodynamic potential at the freezing point is small compared to that of the symmetry conserving part, its role is crucial in stabilizing the crystalline structure and on values of the freezing parameters.

Communication: Integral equation theory for pair correlation functions in a crystal.

A method for calculating pair correlation functions in a crystal is developed. The method is based on separating the one- and two-particle correlation functions into the symmetry conserving and the symmetry broken parts. The conserving parts are calculated using the integral equation theory of homogeneous fluids. The symmetry broken part of the direct pair correlation function is calculated from a series written in powers of order parameters and that of the total pair correlation function from the Ornstein-Zernike equation. The results found for a two-dimensional hexagonal lattice show that the method provides accurate and detailed informations about the pair correlation functions in a crystal.

Correlation functions in liquids and crystals: free-energy functional and liquid-to-crystal transition.

A free-energy functional for a crystal that contains both the symmetry-conserved and symmetry-broken parts of the direct pair-correlation function has been used to investigate the crystallization of fluids in three dimensions. The symmetry-broken part of the direct pair-correlation function has been calculated using a series in ascending powers of the order parameters and which contains three- and higher-body direct correlation functions of the isotropic phase. It is shown that a very accurate description of freezing transitions for a wide class of potentials is found by considering the first two terms of this series. The results found for freezing parameters including the structure of the frozen phase for fluids interacting via the inverse power potential u(r)=ε(σ/r)(n) for n ranging from 4 to ∞ are in very good agreement with simulation results. It is found that for n>6.5 the fluid freezes into a face-centered cubic (fcc) structure while for n≤6 the body-centered cubic (bcc) structure is preferred. The fluid-bcc-fcc triple point is found to be at 1/n=0.158, which is in good agreement with simulation result.

Free-energy functional for freezing transitions: hard-sphere systems freezing into crystalline and amorphous structures.

A free-energy functional that contains both the symmetry-conserved and symmetry-broken parts of the direct pair correlation function has been used to investigate the freezing of a system of hard spheres into crystalline and amorphous structures. The freezing parameters for fluid-crystal transition have been found to be in very good agreement with the results found from simulations. We considered amorphous structures found from molecular dynamics simulations at packing fractions η lower than the glass close packing fraction η(J) and investigated their stability compared to that of a homogeneous fluid. The existence of a free-energy minimum corresponding to a density distribution of overlapping Gaussians centered around an amorphous lattice depicts a deeply supercooled state with a heterogeneous density profile.