Related papers: Attraction between DNA molecules mediated by multi…
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…
We review works on screening of a macroion, such as colloidal particle or double helix DNA, by multivalent counterions. Multivalent metal ions, charged micelles, short or long polyelectrolytes can play the role of multivalent counterions.…
The problem of inhibiting viral DNA ejection from bacteriophages by multivalent counterions, specifically Mg$^{+2}$ counterions, is studied. Experimentally, it is known that MgSO$_4$ salt has a strong and non-monotonic effect on the amount…
We consider a one-dimensional model allowing analytical derivation of the effective interactions between two charged colloids. We evaluate exactly the partition function for an electroneutral salt-free suspension with dielectric jumps at…
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…
We suggest to discriminate single DNA bases via transverse ionic transport, namely by detecting the ionic current that flows in a channel while a single-stranded DNA is driven through an intersecting nanochannel. Our all-atom molecular…
This work investigates the interactions of H-NS proteins and bacterial genomic DNA through computer simulations performed with a coarse-grained model. The model was developed specifically to study the switch of H-NS proteins from the…
We study the spatial and orientational distribution of rodlike counterions (such as mobile nanorods) as well as the effective interaction mediated by them between two plane-parallel surfaces that carry fixed (quenched) heterogeneous charge…
The cations, in form of salt, present in the solution containing DNA play a crucial role in the opening of two strands of DNA. We use a simple non linear model and investigate the role of these cations on the mechanical unzipping of DNA.…
In the present paper we address the general problem of selective electrodynamic interactions between DNA and protein, which is motivated by decades of theoretical study and our very recent experimental findings (M. Lechelon et al,…
In a recent letter [P.K. Shukla and B. Eliasson, Phys. Rev. Lett. 108, 165007 (2012)] the discovery of a new attractive force between protons in a hydrogen plasma was reported that would be responsible for the formation of molecules and of…
The macroscopic curvature induced in double helical B-DNA by regularly repeated adenine tracts (A-tracts) is a long known, but still unexplained phenomenon. This effect plays a key role in DNA studies because it is unique in the amount and…
Electrophoretic (EP) mobility reversal is commonly observed for strongly charged macromolecules in multivalent salt solutions. This curious effect takes place, e.g., when a charged polymer, such as DNA, adsorbs excess counterions so that…
Understanding how the electronic excitation of DNA changes in response to different high-energy particles is central to advancing ion beam cancer therapy. While protons have been the predominant ion of choice in beam cancer therapy, heavier…
The effects of monovalent (Na+, K+) and divalent (Mg2+, Ca2+, Mn2+) ions on the interaction between DNA and histone are studied using the molecular combing technique. Lamda-DNA molecules and DNA-histone complexes incubated with metal…
We study the effective electrostatic interactions between a pair of charged colloidal particles without salt ions while the system is confined in two dimensions. In particular we use a simplified model to elucidate the effects of rotational…
In Molecular Dynamics (MD), the forces applied to atoms derive from potentials which describe the energy of bonds, valence angles, torsion angles, and Lennard-Jones interactions of which molecules are made. These de finitions are classic;…
Despite decades of intensive studies, the effective interactions between strongly charged colloids still remain elusive. Here we show that a strongly charged surface with a layer of condensed counter- ions behaves effectively as a…
We prove that the complex conjugate (c.c.) eigenvalues of a smoothly varying real matrix attract (Eq. 15). We offer a dynamical perspective on the motion and interaction of the eigenvalues in the complex plane, derive their governing…
In this paper we consider dipole-mediated correlations between DNA and enzymes in the context of their water environment. Such correlations emerge from electric dipole-dipole interactions between aromatic ring structures in DNA and in…