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The classical electrostatic interaction between DNA molecules in water in the presence of counterions is reconsidered and we propose it is governed by a modified Poisson-Boltzmann equation. Quantum fluctuations are then studied and shown to…
Interstellar methanol is considered to be a parent species of larger, more complex organic molecules. A physicochemical simulation of infalling parcels of matter is performed for a low-mass star-forming system to trace the chemical…
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between…
The interaction between large internal motion of DNA surrounded by bio-fluid is investigated. The phenomenon is modelled using the relativistic Navier-Stokes lagrangian describing the bio-fluid coupled to the standard Klein-Gordon…
Molecular motor proteins form the basis of cellular dynamics. Recently, notable efforts have led to the creation of their DNA-based mimics, which can carry out complex nanoscale motion. However, such functional analogues have not yet been…
The extent of contact and solvent shared ion pairs of phosphate groups with Na$^+$, Ca$^{2+}$ and Mg$^{2+}$ ions in aqueous environment and their relevance for the stability of polyanionic DNA and RNA structures is highly debated. Employing…
DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…
We present theoretical work in which the degree of electrostatic coupling across a charged lipid bilayer in aqueous solution is analyzed on the basis of nonlinear Poisson-Boltzmann theory. In particular, we consider the electrostatic…
The movement of ionic solutions is an essential part of biology and technology. Fluidics, from nano- to micro- to microfluidics, is a burgeoning area of technology which is all about the movement of ionic solutions, on various scales. Many…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
Solid-state nanopores are promising tools for single molecule detection of both DNA and proteins. In this study, we investigate the patterns of ionic current blockades as DNA translocates into or out of the geometric confinement of such…
Motivation: DNA methylation is an intensely studied epigenetic mark, yet its functional role is incompletely understood. Attempts to quantitatively associate average DNA methylation to gene expression yield poor correlations outside of the…
The association and dissociation of ion pairs in water are fundamental to physical chemistry, yet their reaction coordinates are complex, involving not only interionic distance but also solvent-mediated hydration structures. These processes…
Structural changes in giant DNA induced by the addition of the flexible polymer PEG were examined by the method of single-DNA observation. In dilute DNA conditions, individual DNA assumes a compact state via a discrete coil-globule…
While the thermodynamics of DNA hybridization is well understood, much less is known about the kinetics of this classic system. Filling this gap in our understanding has new urgency because DNA nanotechnology often depends critically on…
The complex mechanisms governing charge migration in DNA oligomers reflect the rich structural and electronic properties of the molecule of life. Controlling the mechanical stability of DNA nanowires in charge transport experiments is a…
DNA methylation is a well-studied genetic modification crucial to regulate the functioning of the genome. Its alterations play an important role in tumorigenesis and tumor-suppression. Thus, studying DNA methylation data may help biomarker…
Functionalization of nanoparticles or colloids is increasingly being used to develop customizable "atoms". Functionalization by attaching single strands of DNA allows for direct control of the binding between nanoparticles, since…
DNA methylation is an epigenetic mechanism that regulates gene expression by adding methyl groups to DNA. Abnormal methylation patterns can disrupt gene expression and have been linked to cancer development. To quantify DNA methylation,…