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Enzymatic DNA labeling is a powerful tool with applications in biochemistry, molecular biology, biotechnology, medical science, and genomic research. This paper contributes to the evolving field of DNA-based data storage by presenting a…
Macromolecular crowding plays a principal role in a wide range of biological processes including gene expression, chromosomal compaction, and viral infection. However, the impact that crowding has on the dynamics of nucleic acids remains a…
We scrutinize the effect of polyvalent ions on polymer-DNA interactions. We extend a recently developed test charge theory to the case of a stiff polymer interacting with a DNA molecule in an electrolyte mixture. The theory accounts for…
Based on non-equilibrium molecular dynamics simulations of entangled polymer melts, a recent Letter [Phys. Rev. Lett. $\textbf{121}$, 047801 (2018), arXiv:1806.09509] claims that the rising extensional stress is quantitatively consistent…
Biological effectiveness of a certain absorbed dose of ionizing radiation depends on the radiation quality, i. e. the spectrum of ionizing particles and their energy distribution. As has been shown in several studies, the biological…
Recent advances in the understanding of the melting behavior of double-stranded DNA with statistical mechanics methods lead to improved estimates of the weight factors for the dissociation events of the chains, in particular for interior…
The precision of biochemical signaling is limited by randomness in the diffusive arrival of molecules at their targets. For proteins binding to the specific sites on the DNA and regulating transcription, the ability of the proteins to…
Recent experimental data indicate that the elastic wormlike rod model of DNA that works well on long length scales may break down on shorter scales relevant to biology. According to Noy and Golestanian (Phys. Rev. Lett. 109, 228101, 2012)…
We demonstrate that a non-perturbative framework for the treatment of the excitations of single walled carbon nanotubes based upon a field theoretic reduction is able to accurately describe experiment observations of the absolute values of…
Nano-scale confinement of polymer in cone-shaped geometries occurs in many experimental situations. A flexible polymer confined in a cone-shaped nano-channel is studied theoretically and using molecular dynamics simulations. Distribution of…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
We show that the problem of describing the conformations of a semiflexible polymer confined to a channel can be mapped onto an exactly solvable model in the so-called extended de Gennes regime. This regime (where the polymer is neither…
It has become clear in recent years that the simple uniform wormlike chain model needs to be modified in order to account for more complex behavior which has been observed experimentally in some important biopolymers. For example, the large…
Polymer networks formed by cross linking flexible polymer chains are ubiquitous in many natural and synthetic soft-matter systems. Current micromechanics models generally do not account for excluded volume interactions except, for instance,…
Experiments show that macromolecular crowding modestly reduces the size of intrinsically disordered proteins (IDPs) even at volume fraction ($\phi$) similar to that in the cytosol whereas DNA undergoes a coil-to-globule transition at very…
We present a perturbation theory to find the response of an anisotropic DNA to the external tension. It is shown that the anisotropy has a nonzero but small contribution to the force-extension curve of the DNA. Thus an anisotropic DNA…
We expand the blob theory for freely-jointed chains and perform molecular dynamics simulations to study the behavior of polymers confined in cylindrical channels. From weak to strong confinement, five scaling regimes, de Gennes, extended de…
We study the Landau damping of the surface plasmon resonance of metallic nanoparticles embedded in different environments of experimental relevance. Important oscillations of the plasmon linewidth as a function of the radius of the…
In the Onsager model of one-component hard-particle systems, the entire phase behaviour is dictated by a function of relative orientation, which represents the amount of space excluded to one particle by another at this relative…
We consider the influence of electrostatic forces on driven translocation dynamics of a flexible polyelectrolyte being pulled through a nanopore by an external force on the head monomer. To this end, we augment the iso-flux tension…