Ring opening reaction of 1,3-cyclohexadiene studied by semiclassical dynamics simulation

A semiclassical dynamics simulation study is reported for the ring opening reaction of 1,3-cyclohexadiene (CHD) triggered by a femtosecond-scale laser pulse. The results clearly demonstrate that, following the excitation by the laser pulse, the ring opening occurs at ∼110 fs and the molecule decays to the ground electronic state at ∼210 fs due to non-adiabatic transition of electrons from LUMO to HOMO orbitals. Isomerization of the product of the ring opening reaction, 1,3,5-hexatriene (HT), to various stable isomers are also well demonstrated by the simulations.     

Molecular Dynamics Simulation of Bubble Nucleation in Explosive Boiling

Molecular dynamics （MD） simulation is carried out for the bubble nucleation of liquid nitrogen in explosive boiling. The heat is transferred into the simulation system by rescaling the velocity of the molecules. The results indicate that the initial equilibrium temperature of liquid and molecular cluster size affect the energy conversion in the process of bubble nucleation. The potential energy of the system violently varies at the beginning of the bubble nucleation, and then varies around a fixed value. At the end of bubble nucleation, the potential energy of the system slowly increases. In the bubble nucleation of explosive boiling, the lower the initial equilibrium temperature, the larger the size of the molecular cluster, and the more the heat transferred into the system of the simulation cell, causing the increase potential energy in a larger range.     

Molecular dynamics simulation on boron diffusion in diamond

The atomic-scale diffusion mechanism of boron in diamond is investigated by molecular dynamics simulation. A substitutional boron atom diffuses to the self-interstitial site when there exists a self-interstitial carbon atom in its nearest tetrahedral center and the system temperature is high. More important, the bond between boron and the self-interstitial carbon atom is never broken during the diffusion process, indicating that B_s-C_i pairs diffuse in the lattice by the interstitial mechanism. The results suggest that boron diffusion is mediated by carbon self-interstitial and not by the vacancy mechanism. In addition, the estimated activation energy and the diffusion exponential prefactor of boron diffusion in diamond are found to be 0.23 eV and 1.123×10⁻⁶cm²/s, respectively.     

Effect of the Carbon-Nanotube Length on Water Permeability

Effect of the carbon nanotube （CNT） channel length on the water flow through the CNT is studied using molecular dynamics simulations. The water flow is found to decay with the channel length （-1/N^2.3, N is the number of carbon rings along the nanotube axis）, much faster than that predicted by a previous continuous-time random walk （CTRW） model （-1/N）. This unexpected decay rate of flow is found to result from the weakening of the correlation of the concerted motion of the water molecules inside the ONT. An improved CTRW model is then proposed by taking into account of this effect. Meanwhile, the diffusion constant of water molecules inside CNTs with various lengths is found to be relatively invariant, which results in a relatively constant hopping rate.     

Correlation between Chaotic Dynamics and Level Spacings： the Lyapunov and Dixon Dip Approaches to Highly Excited Vibration of Deuterium Cyanide

Chaotic dynamics of highly excited vibration of deuterium cyanide is explored by two independent approaches： （1） the Lyapunov analysis, based on the classical phase space for the levels, and （2） the Dixon dip analysis based on the concepts of pendulum dynamics and quantized levels. The results show that there is evident correlation between these two algorithms. We also propose that the reciprocal of energy difference between two nearby Dixon dips can be taken as a qualitative measure for the degree of dynamical chaos.     

Double-Exponentially Decayed Photoionization in CREI Effect： Numerical Experiment on 3D H2^＋

On the platform of the 3D H2^＋ system, we perform a numerical simulation of its photoionization rate under excitation of weak to intense laser intensities with varying pulse durations and wavelengths. A novel method is proposed for calculating the photoionization rate： a double exponential decay of ionization probability is best suited for fitting this rate. Confirmation of the well-documented charge-resonance-enhanced ionization （CREI） effect at medium laser intensity and finding of ionization saturation at high light intensity corroborate the robustness of the suggested double-exponential decay process. Surveying the spatial and temporal variations of electron wavefunctions uncovers a mechanism for the double-exponentially decayed photoionization probability as onset of electron ionization along extra degree of freedom. Henceforth, the new method makes clear the origins of peak features in photoionization rate versus internuclear separation. It is believed that this multi-exponentially decayed ionization mechanism is applicable to systems with more degrees of motion.     

An empirical model for free surface energy of strained solids at different temperature regimes

We have developed an empirical formulation, based on the elastic theory, to calculate the variation of the surface free energy when a crystal is strained in the elastic regime. The model permits to obtain the variation of the surface energy at different strains and temperatures when are known the thermal dependence on the bulk and surface elastic constants. Molecular dynamics (MD) simulations were performed using the three low index surfaces of Al, to validate the accuracy of the model. The comparison between the empirical model and the MD simulations shows a good agreement for temperatures ranging between 0 and 900 K, and for deformation between −2% and 2%.     

A molecular dynamics study of boron and nitrogen in diamond

Based upon molecular dynamics simulation via the Tersoff many-body potential, we proposed the co-doping method for fabricating n-type diamond. We calculated the optimal co-doping configurations of n-type (nitrogen) and p-type (boron) dopants, the stable structure of a boron atom in diamond is associated with four nitrogen atoms placed at the nearest neighbour positions, the total energy of the system with the stable structure is 136 MeV lower than that of the system with the nitrogen atoms placed in others positions. The results indicated that the co-dopants of nitrogen and boron were the perfect candidates to make n-type diamond, and additional boron would increase the solubility limit of nitrogen in diamond, reduce the lattice-relaxation energy of crystal and improve its doping efficiency in diamond.     

Theory of complete orthonormal sets of relativistic tensor wave functions and Slater tensor orbitals of particles with arbitrary spin in position, momentum and four-dimensional spaces

Using the complete orthonormal basis sets of nonrelativistic and quasirelativistic orbitals introduced by the author in previous papers for particles with arbitrary spin the new analytical relations for the 2(2s+1)-component relativistic tensor wave functions and Slater tensor orbitals in position, momentum and four-dimensional spaces are derived, where s=1/2,1,3/2,2,… . The relativistic tensor function sets are expressed through the corresponding nonrelativistic and quasirelativistic orbitals. The analytical formulas for overlap integrals over relativistic Slater tensor orbitals in position space are also derived.     

Effect of Vibration on Water Transport through Carbon Nanotubes

We study the response of water permeation properties through a carbon nanotube on the time-dependent mechanical signals. It is found that there is a critical frequency of vibrating fc （about 1333 GHz） which plays a significant role in the water permeation properties. The total water flow, the net flux, the number of hydrogen bonds and the dipole flipping frequency of the single-file water chain inside the nanotube are almost unchanged for the frequency of vibrating f 〈 fc. Simulation results show that the nanotube can be effectively resistant to the mechanical noise. Such excellent effect of noise screening is attributed to the exceptional property of water molecules connected by strong hydrogen bonds with each other and forming a one-dimensional water chain inside the nanotube. Our findings are important for the understanding of why biological systems can achieve accurate information transfer in an environment full of fluctuations.     

Impact of Viscosity on DNA Dynamics

We study the influence of viscosity on DNA dynamics. By employing the nonlinear Peyrard-Bishop-Dauxois （PBD） model, it is shown that the DNA dynamics can be explained by a solution of a complex nonlinear Schrǒdinger equation （CNLSE）. This is the nonlinear Schrǒdinger equation （NLSE） with a nonlinear parameter being a complex number. We compare real and imaginary parts of this nonlinear parameter and show that the latter one should not be negligible, which means that the CNLSE should be solved numerically,     

Local structure changes of 54-, 55-, 56-atom copper clusters on heating

The local structure changes among three types of Cu clusters containing 54-56 atoms at elevated temperatures have been studied by employing molecular-dynamics simulations. The simulations show sensitivities of structural changes to different structures of the three clusters with icosahedron-based geometries by removing or adding one atom from a complete icosahedron cluster, and how the structural changes can strongly cause internal energy to change accordingly. Because of the different structures of these clusters, the structure change processes of these types are quite different on heating.     

Electronic structure and driving forces in α-cyclodextrin:butylparaben inclusion complexes

We investigate the geometry and electronic structure for complexes of α-cyclodextrin with butylparaben using DFT and Hartree-Fock calculations. The effect of solvent is explicitly taken into account. A Morokuma-Kiatura analysis of the bond energy is performed. We emphasize the role of the water, by pointing out the changes in the solvent's electronic structure for different docking geometries.     

Absence of Charge-Resonance-Enhanced Ionization in Attosecond Pulse Photoionization： Numerical Result on One-Dimensional H2^＋

We present a numerical result of photoionization rate for the one-dimensional molecular hydrogen ion model exposed to intense light of 1 × 10^16-2×10^16 W/cm^2, 55-as pulse duration, and 800nm wavelength. In contrast to the previous calculation result of charge-resonance-enhanced ionization for lower intensity and much longer pulse, our result exhibits an ionization saturation. The numerical results are interpreted in the field-dressed potential picture as over-the-barrier liberation of electrons. This extremely short pulsewidth and relatively high field phenomenon requests experimental demonstration.     

Effect of temperature on polaron dynamics in poly-DNA

We investigate the effect of temperature on polaron dynamics in the framework of a tight-binding model. The dissociation of a polaron will become fast with the increase of temperature. There exists a crossover of the charge localization time from strong to weak temperature-dependence. Instead of the uniform motion at zero temperature, a polaron moves un-uniformly under a driven field at a finite temperature, which indicates a discrete hopping between base pairs. It is also found that the polaron motion is thermally activated. A high temperature will result in a fast movement of a polaron under a deriving field.     

First-Principles Calculations for Structures and Melting Temperature of Si6 Clusters

We investigate the structures and the melting temperature of the Si6 cluster by using the first-principles pseudopotential method in real space and Langevin molecular dynamics. It is shown that the ground structure of the Si6 cluster is a square bipyramid, and the corresponding melting temperature is about 1923 K. In the heating procedure, the structures of the Si6 cluster change from high symmetry structures containing 5-8 bonds, via prolate structures containing 3-4 bonds, to oblate structures containing 1-2 bonds.     

Dynamical aspects and the role of IVR for the reactivity of noble metal clusters towards molecular oxygen

Here, we present the dynamical aspects and the role of internal energy redistribution (IVR) in the reactivity of noble metal clusters towards O₂. We show on the example of Ag₃O₂ ^- / Ag₃O₂ / Ag₃O₂ ⁺ that NeNePo spectroscopy carried out under zero electron kinetic energy (ZEKE) conditions can be a powerful tool to investigate the geometry relaxation and IVR induced by photodetachment in real time. Furthermore, we demonstrate that difference in the reactivity of Ag₆ ^- and Au₆ ^- towards O₂ can be attributed to different nature of the IVR process. Dissipative IVR in Ag₆ ^- favors fast complex stabilization, whereas resonant IVR found for Au₆ ^- might be an important factor determining the catalytic activity of Au₆ ^- cluster in the CO oxidation.     

Influence of surface treatments on the shear bond strength of orthodontic brackets to porcelain

The purpose of this study was to investigate the effect of various surface treatments after different storage time and thermocycling on the shear bond strength of orthodontic brackets to the feldspathic porcelain surfaces. 128 disc-shaped porcelain specimens were randomly assigned to the following surface treatments: 9.6% HFA, 9.6% HFA combined with silane, 50 μ aluminum trioxide sandblasting followed by silane and application of silane after 37% phosphoric acid. Metal or ceramic brackets were bonded onto each treated porcelain facet with light cured resin. The samples were stored in 37 °C water 1 day or 7 days, thermocycled 500 times from 5 to 55 °C. The shear bond strengths were measured (1 mm/min), and statistically analyzed. The bond failure sites were classified according to ARI system. The surface of the glazed, sandblasted, hydrofluoric and phosphoric acid etched porcelain were examined with SEM. All groups achieved reasonable bond strengths to withstand the application of orthodontic forces. Water storage for 7 days caused lower shear bond strength than that of 1 day. But there is no statistically significant difference between the two groups. The mean shear bond strength provided by ceramic bracket with mechanical retention had no statistical difference with that of metal bracket. Therefore, the optimal treatment for orthodontic brackets bonding to feldspathic porcelain was to apply phosphoric acid combined with silane.     

Molecular dynamics simulation of the solidification of liquid gold nanowires

The solidification behavior of liquid gold nanowires with about 1.84 nm in diameter has been studied by using molecular dynamics simulation with an embedded atom potential. It is found the cooling rate has great effect on the final structure of the gold nanowires during solidification from liquid. With the decrease of cooling rates, the final structure of the gold nanowires varies from amorphous to crystalline via helical multi-shelled structure. The face-centered cubic structure of the gold nanowires is proven energetically the most stable form.     

A study of Barstar folding events using boundary value simulations

From extensive biophysical studies of protein folding, two competing mechanisms emerged: hydrophobic collapse and the framework model. Our protein of choice is Barstar—a barnase inhibitor. The approximation algorithm we used to study Barstar folding trajectories is called SDEL—stochastic difference equation in length. Using the native structure as the final boundary value and a collection of unfolded structures as the varying initial boundary value, SDEL calculates an ensemble of least action pathways between these boundaries. The results are atomically detailed folding pathways, with as many intermediate structures as you request in the input. We generated 12 pathways, starting from a structurally wide selection of unfolded conformations. Using the protein's radius of gyration as our primary reaction coordinate, we tracked H-bonds, dihedral angles, native and non-native contacts, and energy along the folding pathways. This paper will follow our findings, with special emphasis on pinpointing hydrophobic collapse as a more appropriate mechanism for Barstar. Comparison with pathway predictions for Barstar using experimental techniques will also be discussed.