相关论文: Helix-coil Transition in Closed Circular DNA

A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely…

We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with…

A model for the information transfer from DNA to protein using quantum information and computation techniques is presented. DNA is modeled as the sender and proteins are modeled as the receiver of this information. On the DNA side, a…

We demonstrate rotational excitation of molecular ions that are sympathetically cooled by laser-cooled atomic ions to a temperature as low as ca. 10 mK. The molecular hydrogen ions HD+ and the fundamental rotational transition $(v=0,\,…

We study in this paper mechanisms of hadron melting based on the spectral representation of hadronic quantum channels, and examine the hadron width dependence of the pressure. The findings are applied to a statistical hadron model of QCD…

The electronic structure of an infinite poly-guanine - poly-cytosine DNA molecule in its dry A-helix structure is studied by means of density-functional calculations. An extensive study of 30 nucleic base pairs is performed to validate the…

The tunneling Hamiltonian describes a particle transfer from one region to the other. While there is no particle storage in the tunneling region itself, it has associated certain amount of energy. We name the corresponding flux energy…

A Hamiltonian dynamics is defined for the XY model by adding a kinetic energy term. Thermodynamical properties (total energy, magnetization, vorticity) derived from microcanonical simulations of this model are found to be in agreement with…

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…

We study the tautomeric transitions in base pairs of DNA considering elastic properties of DNA as classical and tunneling of protons as quantum, and show that the dynamics of the transitions admits of soliton like solutions whose shape and…

We investigate, for the first time, the thermal signature of a single-stranded helical molecule that is described beyond usual nearest-neighbor electron hopping, by analyzing electronic specific heat. Depending on the hopping of electrons,…

We recently proposed a dynamical mesoscopic model for DNA, which is based, like statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present article, we first describe how the parameters of this model are…

A statistical method is developed to estimate the maximum amplitude of the base pair fluctuations in a three dimensional mesoscopic model for nucleic acids. The base pair thermal vibrations around the helix diameter are viewed as a Brownian…

The coil-globule transition has been studied for A-B copolymer chains both by means of lattice Monte Carlo simulations using bond fluctuation algorithm and by a numerical self-consistent field method. Copolymer chains of fixed length with A…

OpenMC can be used to computationally model depletion and produce estimates of decay heat. As an input to depletion simulations, OpenMC requires a depletion chain that details nuclide transmutation pathways. The simplified CASL depletion…

We develop a thermodynamically consistent chemo-thermo-mechanical model for the $\beta\rightarrow\delta$ phase transition of energetic HMX crystals. In contrast to previous models, which either considered specific heat to be a constant or…

Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…

This presentation starts with a brief review of our current picture of QCD phases, derived from lattice QCD thermodynamics and from models based on the symmetries and symmetry breaking patterns of QCD. Typical approaches widely used in this…

In this work we report the study of conformation dependent electronic transport properties of DNA double-helix within tight-binding framework including its helical symmetry. We have studied the changes in localization properties of DNA as…

Conventional molecular dynamics simulation has been used to determine melting temperature of highly compressed classical molecular hydrogen in a wide range of pressures and temperatures using non-empirical atom-atom potentials…