Related papers: Dynamical Scaling and Phase Coexistence in Topolog…
Near the melting transition the bending elastic constant, $\kappa$, an emergent property of double-stranded DNA (dsDNA), is shown not to follow the rod-like scaling for small length $N$. The reduction in $\kappa$ with temperature is…
Many thermodynamic instabilities in one dimension (e.g. DNA thermal denaturation, wetting of interfaces) can be described in terms of simple models involving harmonic coupling between nearest neighbors and an asymmetric on-site potential…
We report a molecular dynamics simulation of a supercooled simple monatomic glass-forming liquid. It is found that the onset of the supercooled regime results in formation of distinct domains of slow diffusion which are confined to the…
The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions…
Spontaneous liquid-liquid phase separation is commonly understood in terms of phenomenological mean-field theories. These theories correctly predict the structural features of the fluid at sufficiently long time scales and wavelengths.…
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…
The hypothesis that phase transitions originate from some topological change of the critical level hypersurface of the potential energy receives direct evident support by our study of the Bishop--Peyrard model of DNA thermal denaturation.
We study analytically the intricate phase behavior of cross-linked $AB$ diblock copolymer melts, which can undergo two main phase transitions due to quenched random constraints: Gelation, i.e., spatially random localization of polymers…
Even though our theoretical understanding of dendritic solidification is relatively well developed, our current ability to model this process quantitatively remains extremely limited. This is due to the fact that the morphological…
We investigate melting transition of DNA sequences embedded in a Langevin fluctuation-dissipation thermal bath. Torsional effects are considered by a twist angle $\varphi$ between neighboring base pairs stacked along the molecule backbone.…
In many biopolymer solutions, attractive interactions that stabilize finite-sized clusters at low concentrations also promote phase separation at high concentrations. Here we study a model biopolymer system that exhibits the opposite…
In the nuclei of eukaryotic cells, DNA is packaged through several levels of compaction in an orderly retrievable way that enables the correct regulation of gene expression. The functional dynamics of this assembly involves the unwinding of…
By combining analytical theory and Molecular Dynamics simulations we study the relaxation dynamics of DNA circular plasmids that initially undergo a local twist perturbation. We identify three distinctive time scales; (I) a rapid relaxation…
Several controversial issues concerning the packing of linear DNA in bacteriophages and globules are discussed. Exact relations for the osmotic pressure, capsid pressure and loading force are derived in terms of the hole size inside phages…
Experimental studies of the thermal denaturation of DNA yield a strong indication that the transition is first order. This transition has been theoretically studied since the early sixties, mostly within an approach in which the microscopic…
The preferential formation of one solid over the other, as it precipitates out from the melt at specific temperatures, is often explained by invoking a competition between thermodynamic and kinetic control. A quantitative theory, however,…
We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…
A unified model is constructed to study the recently observed DNA entropic elasticity, cooperative extensibility, and supercoiling property. With the introduction of a new structural parameter (the folding angle $\phi$), bending…
The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for…
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accurately separate different topoisomers of a molecule, a full…