Both tetrahydrofuran （THF） and 2-methyltetrahydrofuran （MTHF） are studied systematically at desired temperatures using molecular dynamics simulations. The results show that the calculated densities are well consistent with experiment. Their glass transition temperatures are obtained： 115 K - 130 K for THF and 131 K - 142 K for MTHF. The calculated results from the dipolar orientational time correlation functions indicate that the ＂long time＂ behavior is often associated with a glass transition. From the radial and spatial distributions, we also find that the methyl has a direct impact on the structural symmetry of molecules, which leads to the differences of physical properties between THF and MTHF.
The adenine-thymine base pair was studied in the presence of hydroxyl radicals in order to probe the hydrogen bond effect. The results show that the hydrogen bonds have little effect on the hydroxylation and dehydrogenation happened at the sites, which are not involved in a hydrogen bond, while at the sites involved in hydrogen bond formation in the base pair, the reaction becomes more difficult, both in view of the free energy barrier and the exothermicity. With a 6-311 ＋＋G（d,p） level of description, both B3LYP and MP2 methods confirm that the C8 site of isolated adenine has the highest possibility to form covalent bond with the hydroxyl radicals, though with different energetics： B3LYP predicts a barrierless pathway, while MP2 finds a transition state with an energy of 106.1 kJ/mol. For the dehydrogenation reactions, B3LYP method predicts that the free energy barrier increases in the order of HN9 〈 HN61 〈 HN62 〈 H2 〈 H8.
Molecular dynamics simulations are performed to investigate the polymorphism and flexibility of DNA in water,ethylene glycol(EG)and ethanol(EA)solutions.DNA in EG resembles the structure of DNA in water exhibiting B-DNA.In contrast,the DNA is an A-DNA state in the EA.We demonstrate that one important cause of these A$\leftrightarrow$B state changes is the competition between hydration and direct cation coupling to the phosphate groups on DNA backbones.To DNA structural polymorphism,it is caused by competition between hydration and cation coupling to the base pairs on grooves.Unlike flexible DNA in water and EA,DNA is immobilized around the canonical structure in EG solution,eliminating the potential biological effects of less common non-canonical DNA sub-states.
The isospin effects of projectile fragmentation at intermediate energies are investigated using an isospin-dependent Boltzmann-Langevin model.The collisions of mass-symmetric reactions including 58Fe,58Ni+58Fe,and Ni at intermediate energies,in the 30 to 100 MeV/A range,are studied for different symmetry energies.Yield ratios of the isotopic,isobaric,and isotonic pairs of fragments from the intermediate-mass region using three symmetry energies are extracted as functions of the N/Z ratio of the composite systems in the entrance channel and the incident energies.It is found that the yield ratios are sensitive to symmetry energies,especially for neutron-rich systems,and the calculations using soft symmetry energy are closer to the experimental data.The isospin effect is stronger for the soft symmetry energy,owing to the competition of the repulsive Coulomb force and the symmetry energy attractive force on the proton.For the first time,the splits are presented,revealing a transition from the isospin equilibrium at lower energies to translucency at intermediate energies.The results show a degree of transparency in that intermediate mass fragments undergo a transition from dependence on the composite systems in the entrance channel to reliance on the projectile and target nuclei.
β-decay half-lives of some magic and semi-magic nuclei have been studied in a fully self-consistent Skyrme Hartree-Fock(HF) plus charge-exchange random phase approximation(RPA).The self-consistency is addressed,in that the same Skyrme energy density functional is adopted in the calculation of ground states and Gamow-Teller excited states.First,the impact of J2 terms on the β-decay half-lives is investigated by using the SGII interaction,revealing a large influence.Subsequently,numerical calculations are performed for the selected nuclei with Skyrme energy density functionals SGII,LNS,SKX,and SAMi.Finally,comparisons to available experimental data and predictions of different theoretical models are discussed.
We study the properties of the ethylene glycol solutions and the conformational transitions of DNA segment in the ethylene glycol solutions by molecular dynamics simulations based on GROMACS. The hydrogen network structures of water–water and ethylene glycol–water are reinforced by ethylene glycol molecules when the concentrations of the solutions increase from 0% to 80%. As illustrated by the results, conformation of the double-stranded DNA in ethylene glycol solutions, although more compact, is similar to the structure of DNA in the aqueous solutions. In contrast, the DNA structure is an A–B hybrid state in the ethanol/water mixed solution. A fraying of terminal base-pairs is observed for the terminal cytosine. The ethylene glycol molecules preferentially form a ring structure around the phosphate groups to influence DNA conformation by hydrogen interactions, while water molecules tend to reside in the grooves. The repulsion between the negatively charged phosphate groups is screened by ethylene glycol molecules, preventing the repulsion from unwinding and extending the helix and thus making the conformation of DNA more compact.
The temperature of fragmenting source in central heavy-ion collisions at Fermi energy is investigated by the isospin-dependent quantum molecular dynamics model in combination with the statistical decay model GEMINI.Five different nuclear thermometers are used to extract nuclear temperature.We find that the He and Li isotope temperature reaches a plateau at about 70-100 MeV/nucleon of beam energy.The slope temperature and the quadrupole fluctuation temperature give high values.The quantum slope temperature and the quantum quadrupole fluctuation temperature are more close to the He and Li isotope temperatures.
