Related papers: Attraction between DNA molecules mediated by multi…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
Motivated by recent experiments we have studied the optical conductivity of DNA in its natural environment containing water molecules and counter ions. Our density functional theory calculations (using SIESTA) for four base pair B-DNA with…
DNA is structurally and mechanically altered by the binding of intercalator molecules. Intercalation strongly affects the force-extension behavior of DNA, in particular the overstretching transition. We present a statistical model that…
DNA adsorption and naturation is modeled via two interacting flexible homopolymers coupled to a solid surface. DNA denatures if the entropy gain for unbinding the two strands overcomes the loss of binding energy. When adsorbed to a surface,…
A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss)…
The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between…
We consider voltage-driving DNA translocation through a nanopore in the present study. By assuming the DNA is coaxial with the cylindrical nanopore, a hydrodynamic model for determining effective force on a single DNA molecule in a nanopore…
In recent years, short DNA duplexes have been studied as an interesting self-assembling system and a building block for DNA-based nanotechnologies. Numerical simulation studies for the determination of the full phase diagram of short…
Charged soft-matter systems--such as colloidal dispersions and charged polymers--are dominated by attractive forces between constituent like-charged particles when neutralizing counterions of high charge valency are introduced. Such…
It is shown that the attractive force between ions in a degenerate quantum plasma, recently predicted by Shukla and Eliasson [Shukla, Eliasson, PRL 108, 165007 (2012), arXiv:1112.5556] using a generalized quantum hydrodynamical model, is…
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
We calculate the force between two spherical metal nanoparticles of charge Q 1 and Q 2 in a dilute 1:1 electrolyte solution. Numerically solving the non-linear Poisson-Boltzmann equation, we find that metal nanoparticles with the same sign…
Like-charge attraction, driven by ionic correlations, challenges our understanding of electrostatics both in soft and hard matter. For two charged planar surfaces confining counterions and water, we prove that even at relatively low…
We deduced the torque applied on a single stretched and twisted DNA by integrating with respect to force the change in the molecule's extension as it is coiled. While consistent with previous direct measurements of the torque at high forces…
We analyse the appearance of a mechanical torque that acts on a chiral molecule: a single-stranded DNA, in which the spin-orbit interaction is expected to induce a spin-selectivity effect. The mechanical torque is shown to appear as a…
Molecules show a much increased multiple ionization rate in a strong laser field as compared to atoms of similar ionization energy. A widely accepted model attributes this to the action of the joint fields of the adjacent ionic core and the…
The mechanism of threshold elongation (overstretching) of DNA macromolecules under the action of external force is studied within the framework of phenomenological approach. When considering the task it is taken into account that…
We present a theoretical description of the effect of polyvalent ions on the interaction between titratable macro-ions. The model system consists of two point-like macro-ions with dissociable sites, immersed in an asymmetric ionic mixture…
DNA condensation by multivalent cations plays a crucial role in genome packaging in viruses and sperm heads, and has been extensively studied using single-molecule experimental methods. In those experiments, the values of the critical…
The existence of attractions between like-charged colloids immersed in ionic solution have been discovered in recent experiments. This phenomenon contradicts the predictions of DLVO theory and indicates a failure of mean field theory. We…