Related papers: Coarse-grained models for phase separation in DNA-…
When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on…
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…
We develop an analytical theory that accounts for the image and surface charge interactions between a charged dielectric membrane and a DNA molecule translocating through the membrane. Translocation events through neutral carbon-based…
Multivalent interactions between deformable mesoscopic units are ubiquitous in biology, where membrane macromolecules mediate the interactions between neighbouring living cells and between cells and solid substrates. Lately, analogous…
While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule…
We study a model for pair interaction $U$ of DNA molecules generated by the discrete dipole moments of base-pairs and the charges of phosphate groups, and find noncommutative group of eighth order ${\cal S}$ of symmetries that leave $U$…
The proper design of DNA sequences allows for the formation of well defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to…
We theoretically study mixtures of chemically-interacting particles, which produce or consume a chemical to which they are attracted or repelled, in the most general case of many coexisting species. We find a new class of active phase…
Motivated by the idea that intrinsically disordered proteins (IDPs) condense into liquid-like droplets within cells, we carry out Monte Carlo simulations of a polymer lattice model to study the relationship between charge patterning and…
At the cutting edge of materials science, matter is designed to self-organize into structures that perform a wide range of functions. The past two decades have witnessed major innovations in the versatility of building blocks, ranging from…
We have studied the extended Hubbard model with pair hopping in the atomic limit for arbitrary electron density and chemical potential. The Hamiltonian considered consists of (i) the effective on-site interaction U and (ii) the intersite…
The osmotic coefficient of B-DNA in water may, in moderately dilute solutions, deviate as much as 100 % from predictions based on a simple 'counterion condensation' theory. We determine the results for osmotic properties via a cell model…
Recent theoretical studies found that mixtures of active and passive colloidal particles phase separate but only at very high activity ratio. The high value poses serious obstacles for experimental exploration of this phenomenon. Here we…
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…
The dynamic behavior of semi-dilute polymer solutions is governed by an interplay between solvent quality, concentration, molecular weight, and flow type. Semi-dilute solutions are characterized by large fluctuations in concentration,…
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,…
We present micro-rheological measurments of the drag force on colloids pulled through a solution of lambda-DNA (used here as a monodisperse model polymer) with an optical tweezer. The experiments show a violation of the Stokes-Einstein…
We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer…
The presence of nanoparticles in a diblock copolymer leads to changes in the morphology and properties of the matrix and can produce highly organized hybrid materials. The resulting material properties depend not only on the polymer…
We present a comprehensive theoretical and experimental study of the solution phase properties of DNA-based family of nanoparticles - dendrimer-like DNA molecules (DL-DNA). These charged DNA dendrimers are novel macromolecular aggregates,…