Related papers: Ion assisted structural collapse of a single stran…
We study the effective interaction mediated by strongly coupled Coulomb fluids between dielectric surfaces carrying quenched, random monopolar charges with equal mean and variance, both when the Coulomb fluid consists only of mobile…
The electrostatic Schwinger-Dyson equations are derived and solved for an electrolyte mixture composed of mono- and multivalent ions confined to a negatively charged nanoslit. The closure of these equations is based on an asymmetric…
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…
Molecular dynamics simulations are used to study the equilibrium distribution of monovalent ions in a nanopore connecting two water reservoirs separated by a membrane, both for the empty pore and that with a single stranded DNA molecule…
The solvation structures and ion dynamics of CaCl$_2$ aqueous electrolytes have been investigated using ab initio molecular dynamics simulations and molecular dynamics simulations with deep learning potentials. We found multiple solvation…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
We address theoretically aggregation of DNA segments by multivalent polyamines such as spermine and spermidine. In experiments, the aggregation occurs above a certain threshold concentration of multivalent ions. We demonstrate that the…
The effective interaction between two parallel strands of helical bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using computer simulations of the "primitive" model of electrolytes. In particular we study a simple…
In this paper we investigate the effects of varying cation valency and concentration on the rheology of entangled lambda DNA solutions. We show that monovalent cations moderately increase the viscoelasticty of the solutions mainly by…
The influence of the salts KCl, NaCl, and NaI at molar concentrations on the {\alpha}-helical folding kinetics of the alanine-based oligopeptide Ace-AEAAAKEAAAKA-Nme is investigated by means of (explicit-water) molecular dynamics…
We study a complex formation between the DNA and cationic amphiphilic molecules. As the amphiphile is added to the solution containing DNA, a cooperative binding of surfactants to the DNA molecules is found. This binding transition occurs…
Understanding plastic deformation of crystals in terms of the fundamental physics of dislocations has remained a grand challenge in materials science for decades. To overcome this, the Discrete Dislocation Dynamics (DDD) method has been…
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single…
The DNA double helix is a polyanionic macromolecule that in water solutions is neutralized by metal ions (counterions). The property of the counterions to stabilize the water network (positive hydration) or to make it friable (negative…
Salt water is ubiquitous, playing crucial roles in geological and physiological processes. Despite centuries of investigations, whether or not water's structure is drastically changed by dissolved ions is still debated. Based on density…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
Genomic DNA is constantly subjected to various mechanical stresses arising from its biological functions and cell packaging. If the local mechanical properties of DNA change under torsional and tensional stress, the activity of…
We study the behavior of single linear polyelectrolytes condensed by trivalent salt under the action of electric fields through computer simulations. The chain is unfolded when the strength of the electric field is stronger than a critical…
In this review, we address the issue of the electrostatic complexation between charged-neutral diblock copolymers and oppositely charged nanocolloids. We show that nanocolloids such as surfactant micelles and iron oxide magnetic…
DNA supercoiling plays an important role in a variety of cellular processes. The torsional stress related with supercoiling may be also involved in gene regulation through the local structure and dynamics of the double helix. To check this…