相关论文: DNA bubble dynamics as a quantum Coulomb problem

Based on the direct method of molecular dynamics, the temperature dependence of energy, partition function, entropy and free energy, describing the first-order phase transition, is calculated for the classical Peyrard-Bishop-Dauxois model…

To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…

We present new results for the phase space factors involved in double beta decay for beta-beta- transitions to ground states and excited 0+1 states, for isotopes of experimental interest. The Coulomb distortion of the electron wave…

Relative lifetimes of inherent double stranded DNA openings with lengths up to ten base pairs are presented for different gene promoters and corresponding mutants that either increase or decrease transcriptional activity, in the framework…

This article deals with the issues of global-in-time existence and asymptotic analysis of a fluid-particle interaction model in the so-called bubbling regime. The mixture occupies the physical space $\Omega \subset \mathbb{R}^3$ which may…

The presence of a thermodynamic phase of a three-stranded DNA, namely, a mixed phase of bubbles of two bound strands and a single one, is established for large dimensions ($d\geq 5$) by using exact real space renormalization group (RG)…

We study the melting of a double stranded DNA in the presence of stretching forces, via 3D Monte-Carlo simulations, exactly solvable models and heuristic arguments. The resulting force-temperature phase diagram is dramatically different for…

The dynamics of a single quantum state embedded in one or several (quasi-)continua is one of the most studied phenomena in quantum mechanics. In this work we investigate its discrete analogue and consider short and long time dynamics based…

The melting phase diagram of a double-stranded DNA in poor solvent is studied using the pruned and enriched Rosenbluth method on a simple cubic lattice. As the solvent quality is changed from good to poor, there is a non-monotonic change in…

The denaturation of double-stranded DNA as function of force and temperature is discussed. At room temperature, sequence heterogeneity dominates the physics of single molecule force-extension curves starting about 7 piconewtons of below a…

Bending of DNA from a straight rod to a circular form in presence of any of the mono-, di-, tri- or tetravalent counterions has been simulated in strong Coulomb coupling environment employing a previously developed energy minimization…

We study the unexpected high flexibility of short dsDNA which recently has been reported by a number of experiments. Via the Langevin dynamics simulation of our Breathing DNA model, first we observe the formation of bubbles within the…

We study the quantum dynamics of the Bose-Hubbard model on a ladder formed by two rings coupled by tunneling effect. By implementing the Bogoliubov approximation scheme, we prove that, despite the presence of the inter-ring coupling term,…

The distance distribution between complementary base pairs of the two strands of a DNA molecule is studied near the melting transition. Scaling arguments are presented for a generalized Poland-Scheraga type model which includes…

We explore the melting of a lattice DNA in the presence of atmospheric disorder, which mimics the crowded environment inside the cell nucleus, using Monte Carlo simulations. The disorder is modeled by randomly retaining lattice sites with…

We examine the behavior of a model which describes the melting of double-stranded DNA chains. The model, with displacement-dependent stiffness constants and a Morse on-site potential, is analyzed numerically; depending on the stiffness…

We study the non-equilibrium dynamics of two dimensional planar ion Coulomb crystals undergoing a structural buckling transition to a three plane configuration, driven by a reduction of the transverse confining frequency. This phase…

We investigate the entanglement dynamics of two uniformly accelerated atoms with the same acceleration perpendicular to their separation. The two-atom system is treated as an open system coupled with fluctuating electromagnetic fields in…

We generalize the Poland-Scheraga (PS) model to the case of a circular DNA, taking into account the twisting of the two strains around each other. Guided by recent single-molecule experiments on DNA strands, we assume that the torsional…

We perform the first numerical three-dimensional studies of quantum field effects in the Bosenova experiment on collapsing condensates by E. Donley et al. [Nature 415, 39 (2002)] using the exact experimental geometry. In a stochastic…