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DNA is increasingly employed for bio and nanotechnology thanks to its exquisite versatility and designability. Most of its use is limited to linearised and torsionally relaxed DNA but non-trivial architectures and torsionally constrained --…
The electro-osmotic flow (EOF) in a neutral system consisting of an aqueous NaCl solution confined in a nanochannel with two parallel Molybdenum disulfide ($\textrm{MoS}_{\textrm{2}}$) walls and in the presence of an external electric field…
DNA is emerging as an increasingly attractive medium for data storage due to a number of important and unique advantages it offers, most notably the unprecedented durability and density. While the technology is evolving rapidly, the…
Ultrafine particle behavior in electro-hydrodynamic (EHD) flow induced by corona discharge is studied experimentally and numerically. The EHD flow serves as a primary particle aspiration/sampling mechanism, the collector does not require…
Trapping, linearization, and imaging of single molecule DNA is of broad interest to both biophysicists who study polymer physics and engineers who build nucleic acid analyzing methods such as optical mapping. In this study, single DNA…
Efficient water transport through nanostructure membranes is essential for advancing filtration and desalination technologies. In this study, we investigate the flow of water through molybdenum disulfide (MoS$_{2}$) nanopores of varying…
A tandem cell is proposed for DNA sequencing in which an exonuclease enzyme cleaves bases (mononucleotides) from a strand of DNA for identification inside a nanopore. It has two nanopores and three compartments with the structure [cis1,…
Charge transfer in a DNA duplex chain is studied by constructing a system with virtual electrodes connected at the ends of each DNA strand. The systeym is described by the tight-binding model and its transport is analyzed by the transfer…
Continuum simulations become an important tool to uncover the mysteries in nanofluidic experiments. However, fluid flow in simulation models is usually unconsidered. Here, systematical simulations are conducted to provide a quantitative…
Single molecule force spectroscopy of DNA strands adsorbed at surfaces is a powerful technique used in air or liquid environments to quantify their mechanical properties. Although the force responses are limited to unfolding events so far,…
Force-driven translocation of a macromolecule through a nanopore is investigated by taking into account the monomer-pore friction as well as the "crowding" of monomers on the {\it trans} - side of the membrane which counterbalance the…
Ionic transport in nanopores or nanochannels is key to many cellular processes and is now being explored as a method for DNA/polymer sequencing and detection. Although apparently simple in its scope, the study of ionic dynamics in confined…
We present a multiscale approach to the modeling of polymer dynamics in the presence of a fluid solvent. The approach combines Langevin Molecular Dynamics (MD) techniques with a mesoscopic Lattice-Boltzmann (LB) method for the solvent…
Due to its polyionic character the DNA double helix is stable and biologically active only in salty aqueous media where its charge is compensated by solvent counterions. Monovalent metal ions are ubiquitous in DNA environment and they are…
Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments…
When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on…
Electroosmotic flow (EOF) through nanoporous membranes has broad applications in micro- and nanofluidic systems, particularly in biomedical diagnostics and chemical analysis. The use of short nanopores enables high fluid flux, and the…
Cytoskeletal crowding plays a key role in the diffusion of DNA molecules through the cell, acting as a barrier to effective intracellular transport and conformational stability required for such processes as transfection, viral infection,…
We have managed to correlate the stability constants of complex formation, which can be registered in equilibrium state, to the dynamic characteristic of the complex lifetime. Thus, the principal concept of molecular biophysics regarding…