Related papers: A Barrier Penetration Model for DNA Double Strand …
The collective behavior of the shortest DNA oligomers in high concentration aqueous solutions is an unexplored frontier of DNA science and technology. Here we broaden the realm of DNA nanoscience by demonstrating that single-component…
We investigate the motion of two overlapping polymers with self-avoidance confined in a narrow 2d box. A statistical model is constructed using blob free-energy arguments. We find spontaneous segregation under the condition: $L > R_{//}$,…
Analysis of single-molecule micromanipulation experiments of DNA unzipping process shows some features of the force-distance curve, namely two consequent plateaus in the area of ${\sim}12-14pN$ dependent on nucleotide sequence structure, as…
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 general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
We study phase behaviours of lipid--bilayer vesicles functionalised by ligand--receptor complexes made of synthetic DNA by introducing a modelling framework and a dedicated experimental platform. In particular, we perform Monte Carlo…
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 study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model,…
We propose a new method for electrophoretic separation of DNA in which adsorbed polymers are driven over a disordered two-dimensional substrate which contains attractive sites for the polymers. Using simulations of a model for long polymer…
We investigate the behavior of a Bose-Einstein Condensate (BEC) under the influence of a central barrier as the particle number trends towards the thermodynamic limit. In order to perform these studies, we present a novel method which is…
Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs…
Time dependence for barrier penetration is considered in the phase space. An asymptotic phase-space propagator for nonrelativistic scattering on a one - dimensional barrier is constructed. The propagator has a form universal for various…
We report a new doorway mechanism for the dissociative electron attachment to genetic materials. The dipole-bound state of the nucleotide anion acts as the doorway for electron capture in the genetic material. The electron gets subsequently…
DNA inside the cellular environment works under a confined space. An intense research of the transcription and replication of DNA in the confined state is structurally significant to command the self assembly of DNA in a chamber or channel.…
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…
A molecular model is proposed of a bilayer consisting of fully saturated DPPC and mono unsaturated DOPC. The model not only encompasses the constant density within the hydrophobic core of the bilayer, but also the tendency of chain segments…
DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent…
We study the dynamic process of splitting a condensate by raising a potential barrier in the center of a harmonic trap. We use a two-mode model to describe the phase coherence between the two halves of the condensate. Furthermore, we…
Under an external field a double-stranded peptide chain can separate in a fragile or ductile transition. It is usually believed that these two regimes are driven either by chemical and thermal fields, or through non-local mechanical…
A lattice model is used to estimate the self-diffusivity of entangled cyclic and linear polymers in blends of varying compositions. To interpret simulation results, we suggest a minimal model based on the physical idea that constraints…