Related papers: Tautomeric Transitions in DNA
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…
Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…
Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…
Spatial diffusion of particles in periodic potential models has provided a good framework for studying the role of chaos in global properties of classical systems. Here a bidimensional "soft" billiard, classically modeled from an optical…
In the present paper we generalised a phenomenological model developed in \cite{gomo:2005} for the description of magnetostructural phase transitions and related peculiarities of elastic properties in solid oxygen under high pressure and/or…
Clarification of the detailed mechanisms involved in the DNA polymorphism is an important challenge for computational molecular biophysics. This paper reports about reversible A/B transitions in DNA observed in silico in a simulated…
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…
By resorting to a model inspired to the standard Davydov and Holstein-Fr\"ohlich models, in the present paper we study the motion of an electron along a chain of heavy particles modelling a sequence of nucleotides proper to a DNA fragment.…
Polymer topology, which plays a principal role in the rheology of polymeric fluids, and non-equilibrium materials, which exhibit time-varying rheological properties, are topics of intense investigation. Here, we push composites of circular…
Bacterial genomes have been shown to be partitioned into several kilobases long chromosomal domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbors.…
We present analytical and numerical study of discrete breathers identified as localized deformations of valence angles accompanied by change of valence bonds in crystalline polyethylene (PE). It is shown that such breathers can exist inside…
We present a dynamically tunable mechanism of wave transmission in 1D helicoidal phononic crystals in a shape similar to DNA structures. These helicoidal architectures allow slanted nonlinear contact among cylin- drical constituents, and…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
The enterobacteria lambda phage is a paradigm temperate bacteriophage. Its lysogenic and lytic life cycles echo competition between the DNA binding $\lambda$-repressor (CI) and CRO proteins. Here we scrutinize the structure, stability and…
We introduce a novel model for DNA condensation (whip-toroid transition) using the path integral method in the framework of the non-linear sigma model on a line segment. We show that some of its classical configurations exhibit toroidal…
We use X-ray scattering and molecular simulations to investigate the structural properties of complexes of multivalent cationic lipids and DNA molecules. At low mole fraction of neutral lipids (NLs), $\Phi_{\rm NL}$, the complexes show…
Recent single molecule experiments probing the passage process of a short single-stranded DNA (ssDNA) through a membrane channel (translocation) allow to measure the passage time distribution. Building on a recent modelling approach (D. K.…
The ability for real-time control of topological defects can open up prospects for dynamical manipulation of macroscopic properties of solids. A sub-category of these defects, formed by particle dislocations, can be effectively described…
Vortex-antivortex pairs in 2D easy-plane ferromagnets have characteristics of solitons in two dimensions. We investigate numerically and analytically the dynamics of such vortex pairs. In particular we simulate numerically the head-on…