Related papers: Reversible B/A Transitions in Single DNA Molecule …
The proper design of DNA sequences allows for the formation of well defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to…
We present a numerical analysis of a DNA hydrogel that consists of three-valent Y-shaped DNA molecules. The building blocks self-assemble fully reversibly from complementary single-stranded DNA segments. We compare melting curves from both…
Water is essential for the activity of proteins. However, the effect of the properties of water on the behavior of proteins is only partially understood. Recently, several experiments have investigated the relation between the dynamics of…
To explore and react to their environment, living micro-swimmers have developed sophisticated strategies for locomotion - in particular, motility with multiple gaits. To understand the physical principles associated with such a behavioural…
The strength of the spin-orbit interaction relevant to transport in a low dimensional structure depends critically on the relative geometrical arrangement of current carrying orbitals. Recent tight-binding orbital models for spin transport…
We study fully three-dimensional droplets that slide down an incline by employing a thin-film equation that accounts for capillarity, wettability, and a lateral driving force in small-gradient (or long-wave) approximation. In particular, we…
The distinctive characteristics of water, evident in its thermodynamic anomalies, have implications across disciplines from biology to geophysics. Considered a valid hypothesis to rationalize its unique properties, a liquid-liquid phase…
We report a study of DNA (150 bp fragments) conformations in very low added salt $<0.05$mM, across wide DNA concentration range $0.0015\leq c \leq 8$~mM (bp). We found an intermediate DNA conformation in the region $0.05 < c < 1$~mM, by…
The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes…
Bending of DNA from a straight rod to a circular form in presence of any of the mono-, di-, tri- or tetravalent counterions has been simulated in strong Coulomb coupling environment employing a previously developed energy minimization…
We investigate dynamical coupling between water and amino acid side-chain residues in solvation dynamics by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on…
The morphology of DNA is strongly influenced by its surrounding environment, including factors such as pH, salt type and valency, and the presence of polymers. Inorganic salts are known to reduce the DNA chain length through mechanisms like…
Theoretical cross sections for the pressure broadening by hydrogen of rotational transitions of water are compared to the latest available measurements in the temperature range 65-220 K. A high accuracy interaction potential is employed in…
In this article, we demonstrate a method for inducing reversible crystal-to-crystal transitions in binary mixtures of soft colloidal particles. Through a controlled decrease of salinity and increasingly dominating electrostatic…
Explicit molecular dynamics simulations were applied to a pair of amorphous silica nanoparticles in aqueous solution, of diameter 4.4 nm with four different background electrolyte concentrations, to extract the mean force acting between the…
A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…
Molecular dynamics simulations are carried out to explore the dynamical crossover phenomenon in strongly confined and mildly supercooled water in graphene oxide nanopores. In contrast to studies where confinement is used to study the…
We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force…
We report in situ single-molecule measurements of proton-induced double-strand breaks (DSBs) in DNA immersed in water, using real-time fluorescence tracking along the entire proton path, including the Bragg peak region. By chemically…
We report translocation experiments on double-strand DNA through a silicon oxide nanopore. Samples containing DNA fragments with seven different lengths between 2000 to 96000 basepairs have been electrophoretically driven through a 10 nm…