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To investigate the structural dynamics of the homology pairing of polymers, we mod- eled the scenario of homologous chromosome pairings during meiosis in Schizosaccharomyces pombe, one of the simplest model organisms of eukaryotes. We…
Advanced Monte Carlo simulations are used to study the effect of nano-slit confinement on metric and topological properties of model DNA chains. We consider both linear and circularised chains with contour lengths in the 1.2--4.8 $\mu$m…
We consider a molecular channel, in which messages are encoded to the frequency of objects (or concentration of molecules) in a pool, and whose output during reading time is a noisy version of the input frequencies, as obtained by sampling…
The electrical properties of extracellular space around neurons are important to understand the genesis of extracellular potentials, as well as for localizing neuronal activity from extracellular recordings. However, the exact nature of…
Mathew-Fenn et al. (Science (2008) 322, 446-9) measured end-to-end distances of short DNA and concluded that stretching fluctuations in several consecutive turns of the double helix should be strongly correlated. I argue that this…
Field-theoretical method is efficient in predicting the assembling structures of polymeric systems. However, for the polymer/nanoparticle mixture, the continuous density description is not suitable to capture the realistic assembly of…
We investigate the subtle effects of diffuse charge on interfacial kinetics by solving the governing equations for ion transport (Nernst-Planck) with realistic boundary conditions representing reaction kinetics (Butler-Volmer) and…
Electromagnetic resonances play a central role in nanophotonics by enabling efficient confinement of electromagnetic energy and enhanced light-matter interaction. Traditionally, resonant phenomena have been described using platform-specific…
The amount and type of self-entanglement of DNA filaments is significantly affected by spatial confinement, which is ubiquitous in biological systems. Motivated by recent advancements in single DNA molecule experiments based on nanofluidic…
Recent work has shown that the resistive force arising from viscous effects within the pore region could explain [Ghosal, S. Phys. Rev. E. vol. 71, 051904 (2006) and Phys. Rev. Lett. vol. 98, 238104 (2007)] observed translocation times in…
Lasers based on biological materials are attracting an increasing interest in view of their use in integrated and transient photonics. DNA as optical biopolymer in combination with highly-emissive dyes has been reported to have excellent…
We discuss the entropy of a circular polymer under a topological constraint. We call it the {\it topological entropy} of the polymer, in short. A ring polymer does not change its topology (knot type) under any thermal fluctuations. Through…
While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension…
In a recent paper (Commun. Phys. 3, 100) Znidaric studies the growth of higher Renyi entropies in diffusive systems and claims that they generically grow ballistically in time, except for spin-1/2 models in d=1 dimension. Here, we point out…
Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a…
In this paper we analyse the importance of a detailed description of the electronic transitions in ultra-small nanoparticles through the optical response to very small changes of size in systems, whose dimensions are in the subnanometric…
We investigate from first principles screening effects in endohedral complexes when small molecules, characterized by a finite electronic dipole moment, such as HF, LiF, NaCl, and H$_2$O, are encapsulated into different nanoscale cages. We…
Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…
In the present study, the ionic transport and selectivity of electrokinetically-driven flow of power-law fluids in a long pH-regulated rectangular nanochannel are analyzed. The electrical potential and momentum equations are numerically…
Using high-throughput Tethered Particle Motion single molecule experiments, the double-stranded DNA persistence length, $L_p$, is measured in solutions with Na$^+$ and Mg$^{2+}$ ions of various ionic strengths, $I$. Several theoretical…