Related papers: How adsorption influences DNA denaturation
We study theoretically the unzipping of a double stranded DNA from a condensed globule state by an external force. At constant force, we find that the double stranded DNA unzips an at critical force Fc and the number of unzipped monomers M…
This chapter will provide an overview of how characterizing free-energy landscapes can provide insights into the biophysical properties of DNA, as well as into the behaviour of the DNA assemblies used in the field of DNA nanotechnology. The…
We formulate the theory of the perturbation caused by an adsorbate upon the substrate lattice in terms of a local modification of the interatomic potential energy around the adsorption site, which leads to the relaxation of substrate atoms.…
Nucleation of a new phase almost always starts at a surface. This surface is almost always assumed not to change with time. However, surfaces can roughen, partially dissolve and change chemically with time. Each of these irreversible…
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural…
Depletion of the liquid density near a solid surface with a weak long-range fluid-surface interaction was studied by computer simulations of the liquid-vapor coexistence of a LJ fluid confined in slitlike pores. In a wide temperature range…
Cononsolvency is a phenomenon for which the solubility of a macromolecule decreases or even vanishes in the mixture of two good solvents. Although it has been widely applied in physicochemical, green chemical and pharmaceutical industry,…
We study the dynamic properties of a model for wetting with two competing adsorbates on a planar substrate. The two species of particles have identical properties and repel each other. Starting with a flat interface one observes the…
A mesoscopic model for heterogeneous DNA denaturation is developed in the framework of the path integral formalism. The base pair stretchings are treated as one-dimensional, time dependent paths contributing to the partition function. The…
The structure of ionic adsorption layers is studied via a proper thermodynamic treatment of the electrostatic and non-electrostatic interactions between the surfactant ions as well as of the effect of thermodynamic non-locality. The…
We use the "magnetic tweezers" technique to reveal the structural transitions that DNA undergoes in the force-torsion space. In particular, we focus on regions corresponding to negative supercoiling. These regions are characterized by the…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
We generalize the Poland-Scheraga (PS) model to the case of a circular DNA, taking into account the twisting of the two strains around each other. Guided by recent single-molecule experiments on DNA strands, we assume that the torsional…
The experimental results presented in this paper show the influence of the elastic deformation of porous solids on the adsorption process. With p+-type porous silicon formed on highly boron doped (100) Si single crystal, we can make…
The structure and dynamics of negatively charged nucleic acids strongly correlate with the concentration and charge of the oppositely charged counter-ions. It is well known that the structural collapse of DNA is favored in the presence of…
Adsorption at an attractive surface in a system with particles self-assembling into small clusters is studied by Molecular dynamics (MD) simulation. We assume Lennard-Jones plus repulsive Yukawa tail interactions, and focus on small…
We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand…
DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system…
Here we derive and experimentally test a free energy functional that captures the adhesion of DNA-coated emulsion droplets. Generalizing previous approaches, the theory combines important energetic and entropic effects of microscopic DNA…
Melting and hybridization of DNA-capped gold nanoparticle networks are investigated with optical absorption spectroscopy. Single-stranded, 12-base DNA-capped gold nanoparticles are linked with complementary, single-stranded, 24-base linker…