用分子动力学模拟甲烷水合物热激法分解

用分子动力学模拟方法研究甲烷水合物热激法分解，系统地研究注入340 K液态水的结构Ⅰ型甲烷水合物的分解机理.模拟显示水合物表层水分子与高温液态水分子接触获得热能，分子运动激烈，摆脱水分子间的氢键束缚，笼状结构被破坏.甲烷分子获得热能从笼中挣脱，向外体系扩散.热能通过分子碰撞从外层传递给内层水分子，水合物逐层分解.对比注入277K液态水体系模拟结果，得出热激法促进水合物分解.

Fusion dynamics of symmetric systems near barrier energies

Within the framework of the improved isospin-dependent quantum molecular dynamics (ImIQMD) model,he fusion dynamics of symmetric reaction systems are investigated systematically. Calculations show that the number of nucleon transfer in the neck region is appreciably dependent on the incident energies, but strongly on he reaction systems. A comparison of the neck dynamics is performed for the symmetric reactions 58Ni+58Niand 64Ni+64Ni at energies in the vicinity of the Coulomb barrier. An increase of the ratios of the neutron to proton in the neck region at initial collision stage is observed and obvious for the latter system, which reduces the fusion barrier of two colliding nuclei. The distribution of the dynamical fusion barriers and the fusion excitation functions are calculated and compared with the available experimental data.

Scaling and the thermal conductivity of the Frenkel-Kontorova model

We have studied the dependence of the thermal conductivity kappa on the strength of the interparticle potential lambda and the strength of the external potential beta in the Frenkel-Kontorova model. We found that the functional relation can be expressed in a scaling form, kappa(proportional to) lambda 3/2/beta(2 center dot). This result is first obtained by nonequilibrium molecular dynamics. It is then confirmed by two analytical methods, the self-consistent phonon theory and the self-consistent stochastic reservoirs method. The thermal conductivity kappa is therefore a decreasing functon of beta and an increasing function of lambda.

Nuclear reaction dynamics induced by halo-nuclei at intermediate energy heavy ion collisions

We studied systematically the reaction dynamics induced by neutron-halo nuclei and proton-halo nuclei within the isospin dependent quantum molecular dynamics, such as the effects of loose bound halo-nuclei on the fragmentation reaction and momentum dissipation for different colliding systems with different beam energies and different impact parameters. In order to emphasize the roles of neutron-halo nucleus B-19 and proton-halo nucleus Al-23 on the reaction dynamics we also calculated the the reaction dynamics induced by the stable nuclei F-19 and Na-23 with equal mass under identical incident channel conditions. Based on the comparison of results of reaction dynamics induced by halo-nucleus colliding systems and stable nucleus collidinmg systems we found that the roles of loose bound halo-nucleus structure on the fragmentation multiplicity and nuclear stopping (momentum dissipation) are important for all of colliding systems with different beam energies and minor impact parameters, such as, the loose bound halo-nuclei structure increases the fragmentation multiplicity, but reduces the nuclear stopping.

Dynamics of strangeness production in heavy-ion collisions near threshold energies

Within the framework of the improved isospin-dependent quantum molecular dynamics (ImIQMD) model, the dynamics of strangeness (K-0,K-+, Lambda, and Sigma(-,0,+)) production in heavy-ion collisions near threshold energies is investigated systematically, with the strange particles considered to be produced mainly by inelastic collisions of baryon-baryon and pion-baryon. Collisions in the region of suprasaturation densities of the dense baryonic matter formed in heavy-ion collisions dominate the yields of strangeness production. Total multiplicities as functions of incident energies and collision centralities are calculated with the Skyrme parameter SLy6. The excitation function of strangeness production is analyzed and also compared with the KaoS data for K+ production in the reactions C-12 + C-12 and Au-197 + Au-197.

Dynamics of pion production in heavy-ion collisions around 1A GeV energies

Within the framework of the improved isospin-dependent quantum molecular dynamics model, the dynamics of pion emission in heavy-ion collisions in the region of 1A GeV energies as a probe of nuclear symmetry energy at suprasaturation densities is investigated systematically. The total pion multiplicities and the pi(-)/pi(+) yields are calculated for selected Skyrme parameters SkP, SLy6, Ska, and SIII and also for the cases of different stiffness of symmetry energy with the parameter SLy6. The influence of Coulomb potential, symmetry energy, and in-medium pion potential on the pion production is investigated and compared to each other by analyzing the distributions of transverse momentum and longitudinal rapidity and also the excitation functions of the total pion and the pi(-)/pi(+) ratio. The directed flow, elliptic flow, and polar-angle distributions are calculated for the cases of different collision centralities and also the various stiffnesses of the symmetry energies. A comparison of the calculations with the available experimental data is performed.

New parameters of many-body potentials: studying the thermal and mechanical properties of noble metals

New parameters of nearest-neighbor EAM (1N-EAM), n-th neighbor EAM (NN-EAM), and the second-moment approximation to the tight-binding (TB-SMA) potentials are obtained by fitting experimental data at different temperatures. In comparison with the available many-body potentials, our results suggest that the 1N-EAM potential with the new parameters is the best description of atomic interactions in studying the thermal expansion of noble metals. For mechanical properties, it is suggested that the elastic constants should be calculated in the experimental zero-stress states for all three potentials. Furthermore, for NNEAM and TB-SMA potentials, the calculated results approach the experimental data as the range of the atomic interaction increases from the first-neighbor to the sixth-neighbor distance.

Bluish-white emission from radical carbonyl impurities in amorphous Al2O3 prepared via the Pechini-type sol-gel process

Many efforts have been devoted to exploring novel luminescent materials that do not contain expensive or toxic elements, or do not need mercury vapor plasma as the excitation source. In this paper, amorphous Al2O3 powder samples were prepared via the Pechini-type sol-gel process. The resulting samples were characterized by X-ray diffraction (XRD), Fourier transform infrared (FT-IR) spectroscopy, field emission scanning electron microscopy (FESEM), photoluminescence (PL) excitation and emission spectra, kinetic decay, and electron paramagnetic resonance (EPR).

First Principles Investigation on the Ultra-Incompressible and Hard TaN

The structural, electronic, and mechanical properties of TaN were investigated by use of the density functional theory (DFT). Eight structures were considered, i.e.. hexagonal WC TaN, NiAs, wurtzite, and CoSn structures. cubic NaCl. zinc-blende and CsCl structures. The results indicate that TaN in TaN-type structure is the most stable at ambient conditions among the considered structures. Above 5 GPa, TaN in WC-type structure becomes energetically the most stable phase. They are also stable both thermodynamically and mechanically. TaN in WC-type has the largest shear Modulus 243 GPa and large bulk modulus 337 GPa among the considered structures. The Volume compressibility is slightly larger than diamond, but smaller than c-BN at pressures from 0 to 100 GPa. The compressibility along the c axis is smaller than the linear compressibility of both diamond and c-BN.

Influence of molecular topology on the static and dynamic properties of single polymer chain in solution

The influence of molecular topology on the structural and dynamic properties of polymer chain in solution with ring structure, three-arm branched structure, and linear structure are studied by molecular dynamics simulation. At the same degree of polymerization (N), the ring-shaped chain possesses the smallest size and largest diffusion coefficient. With increasing N, the difference of the radii of gyration between the three types of polymer chains increases, whereas the difference of the diffusion coefficients among them decreases. However, the influence of the molecular topology on the static and the dynamic scaling exponents is small. The static scaling exponents decrease slightly, and the dynamic scaling exponents increase slightly, when the topology of the polymer chain is changed from linear to ring-shaped or three-arm branched architecture. The dynamics of these three types of polymer chain in solution is Zimm-like according to the dynamic scaling exponents and the dynamic structure factors.

Exploring the mechanism of flexible biomolecular recognition with single molecule dynamics

Combining a single-molecule study of protein binding with a coarse grained molecular dynamics model including solvent (water molecules) effects, we find that biomolecular recognition is determined by flexibilities in addition to structures. Our single-molecule study shows that binding of CBD (a fragment of Wiskott-Aldrich syndrome protein) to Cdc42 involves bound and loosely bound states, which can be quantitatively explained in our model as a result of binding with large conformational changes. Our model identified certain key residues for binding consistent with mutational experiments. Our study reveals the role of flexibility and a new scenario of dimeric binding between the monomers: first bind and then fold.

Energetic basis of molecular recognition in a DNA aptamer

The thermal stability and ligand binding properties of the L-argininamide-binding DNA aptamer (5'-GATCGAAACGTAGCGCCTTCGATC3') were studied by spectroscopic and calorimetric methods. Differential calorimetric studies showed that the uncomplexed aptamer melted in a two-state reaction with a melting temperature T-m = 50.2 +/- 0.2 degrees C and a folding enthalpy Delta H degrees(fold) = -49.0 +/- 2.1 kcal mol(-1). These values agree with values of T-m = 49.6 degrees C and Delta H degrees(fold) = -51.2 kcal mol(-1) predicted for a simple hairpin structure. Melting of the uncomplexed aptamer was dependent upon salt concentration, but independent of strand concentration. The T of aptamer melting was found to increase as L-argininamide concentrations increased. Analysis of circular dichroism titration data using a single-site binding model resulted in the determination of a binding free energy Delta G degrees(bind) = -5.1 kcal mol(-1). Isothermal titration calorimetry studies revealed an exothermic binding reaction with Delta H degrees(bind) = -8.7 kcal mol(-1). Combination of enthalpy and free energy produce ail unfavorable entropy of -T Delta S degrees = +3.6 kcal mol(-1). A molar heat capacity change of -116 cal mol(-1) K-1 was determined from calorimetric measurements at four temperatures over the range of 15-40 degrees C. Molecular dynamics simulations were used to explore the structures of the unligated and ligated aptamer structures.

Interaction between La3+ and MP-11 in the physiological solution

In this paper, the interaction between La3+ and microperoxidase-11 (MP-11) in the imitated physiological solution was investigated with the electrochemical method, circular dichroism (CD) and ultraviolet-visible (UV-vis) absorption spectroscopy. It was found that the interaction ways between La3+ and MP-11 are different with increasing the molar ratio of La3+ and MP-11. When the molar ratio of La3+ and MP-11 is less than 2, La3+ mainly interacts with the metacetonic acid group of the heme group in the MP-11 molecules, causing the increase in the non-planarity of the porphyrin cycle in the heme group and the decrease in the content of the random coil conformation of MP-11. These structural changes would increase the exposure extent of the electrochemical active center of MP-11 and thus, La3+ can promote the electrochemical reaction of MP-11 and its electrocatalytic activity for the reduction of H2O2 at the glassy carbon (GC) electrode. However, when the molar ratio of La3+ and MP-11 is larger than 3, except binding to the carbonyl oxygen of the metacetonic acid group in the heme group, La3+ interacts also with the oxygen-containing groups of the amides in the polypeptide chains of the MP-11 molecules, leading to the increase in the contents of the random coil conformation in the peptide of the MP-11 molecule, comparing with that for the molar ratio of less than 2.

Single-molecule dynamics reveals cooperative binding-folding in protein recognition

The study of associations between two biomolecules is the key to understanding molecular function and recognition. Molecular function is often thought to be determined by underlying structures. Here, combining a single-molecule study of protein binding with an energy-landscape-inspired microscopic model, we found strong evidence that biomolecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse-grained molecular dynamics on the residue level with the energy function biased toward the native binding structure ( the Go model). With our model, the underlying free-energy landscape of the binding can be explored. There are two distinct conformational states at the free-energy minimum, one with partial folding of CBD itself and significant interface binding of CBD to Cdc42, and the other with native folding of CBD itself and native interface binding of CBD to Cdc42. This shows that the binding process proceeds with a significant interface binding of CBD with Cdc42 first, without a complete folding of CBD itself, and that binding and folding are then coupled to reach the native binding state.