Related papers: Ion assisted structural collapse of a single stran…
We present results of molecular dynamics simulations of strong, flexible polyelectrolyte chains in solution with added salt. The effect of added salt on the polyelectrolyte chain structure is fully treated for the first time as a function…
A mechanism of double strand breaking (DSB) in DNA due to the action of two electrons is considered. These are the electrons produced in the vicinity of DNA molecules due to ionization of water molecules with a consecutive emission of two…
Solvation of ions is ubiquitous on our planet. Solvated ions have a profound effect on the behavior of ionic solutions, which is crucial in nature and technology. Experimentally, ions have been classified into "structure makers" or…
DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of…
Screening of a macroion such as a charged solid particle, a charged membrane, double helix DNA or actin by multivalent counterions is considered. Small colloidal particles, charged micelles, short or long polyelectrolytes can play the role…
Properties of polyelectrolytes in tetravalent salt solutions are intensively investigated by a coarse-grained model. The concentration of salt and the size of tetravalent counterions are found playing a decisive role on chain properties. If…
We predict streaming current inversion with multivalent counterions in hydrodynamically driven polymer translocation events from a correlation-corrected charge transport theory including charge fluctuations around mean-field electrostatics.…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
Double-stranded DNA `overstretches' at a pulling force of about 65 pN, increasing in length by a factor of 1.7. The nature of the overstretched state is unknown, despite its considerable importance for DNA's biological function and…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
The design of hydrogels that combine mechanical robustness with dynamic reconfigurability remains a fundamental challenge, as increasing crosslink dissociation rates compromise network integrity. This limitation is addressed through the…
The rupture of double-stranded DNA under stress is a key process in biophysics and nanotechnology. In this article we consider the shear-induced rupture of short DNA duplexes, a system that has been given new importance by recently designed…
Because of the double-helical structure of DNA, in which two strands of complementary nucleotides intertwine around each other, a covalently closed DNA molecule with no interruptions in either strand can be viewed as two interlocked…
Electrostatic properties and stability of charged virus-like nano-shells are examined in ionic solutions with monovalent and multivalent ions. A theoretical model based on a thin charged spherical shell and multivalent ions within the…
As the ultimate miniaturization of semiconductor devices approaches, it is imperative that the effects of single dopants be clarified. Beyond providing insight into functions and limitations of conventional devices, such information enables…
The folding angle distribution of stretched and negatively supercoiled DNA double-helix is investigated based on a theoretical model we proposed earlier [H. Zhou et al., Phys. Rev. Lett. 82, 4560 (1999)]. It is shown that pulling can…
By molecular dynamics simulation, we study the charge inversion phenomenon of a rod macroion in the presence of polyelectrolyte counterions. We simulate electrophoresis of the macroion under an applied electric field. When both counterions…
We investigate the ion distribution and overcharging at charged interfaces with dielectric inhomogeneities in the presence of asymmetric electrolytes containing polyvalent and monovalent ions. We formulate an effective "dressed counterion"…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
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…