Understanding the reaction between muonium atoms and hydrogen molecules: zero point energy,tunnelling, and vibrational adiabaticity

The advent of very precise measurements of rate coefficients in reactions of muonium (Mu), the lightest hydrogen isotope, with H₂ in its ground and first vibrational state and of kinetic isotope effects with respect to heavier isotopes has triggered a renewed interests in the field of muonic chemistry. The aim of the present article is to review the most recent results about the dynamics and mechanism of the reaction Mu+H₂ to shed light on the importance of quantum effects such as tunnelling, the preservation of the zero point energy, and the vibrational adiabaticity. In addition to accurate quantum mechanical (QM) calculations, quasiclassical trajectories (QCT) have been run in order to check the reliability of this method for this isotopic variant. It has been found that the reaction with H₂(v=0) is dominated by the high zero point energy (ZPE) of the products and that tunnelling is largely irrelevant. Accordingly, both QCT calculations that preserve the products’ ZPE as well as those based on the Ring Polymer Molecular Dynamics methodology can reproduce the QM rate coefficients. However, when the hydrogen molecule is vibrationally excited, QCT calculations fail completely in the prediction of the huge vibrational enhancement of the reactivity. This failure is attributed to tunnelling, which plays a decisive role breaking the vibrational adiabaticity when v=1. By means of the analysis of the results, it can be concluded that the tunnelling takes place through the ν₁=1 collinear barrier. Somehow, the tunnelling that is missing in the Mu+H₂(v=0) reaction is found in Mu+H₂(v=1).     

The atomic and molecular reaction statics

This work presents a new science called atomic and molecular reaction statics (AMRS). There are four parts for AMRS, i.e. the group theoretical derivation of molecular electronic states, the principle of microscopic reversibility, the principle of microscopic transitivity and the optimum energy process rule. AMRS has been developed for about twenty years.     

Diffusion activation energy versus the favourable energy in two-order-parameter model:A molecular dynamics study of liquid Al

In the present work, we find that both diffusion activation energy E_a(D) and E_a(S^ex) increase linearly with pressure and have the same slope (0.022±0.001 eV/GPa) for liquid Al. The temperature and pressure dependence of excess entropy is well fitted by the expression -S^ex(T,P)/k_B=a(P)+b(P)T+c(P)exp(E_f/k_BT), which together with the small ratio of E_f/k_BT leads to the relationship of excess entropy to temperature and pressure, i.e. S^ex≈-cE_f/T, where c is about 12 and E_f (=Δ E-PΔV) is the favourable energy. Therefore, there exists a simple relation between E_a(S^ex) and E_f, i.e. E_a(S^ex)≈cE_f.     

Nonequilibrium dynamics of a diffusion-limited reaction driven by a cluster-memory mechanism

The diffusion-limited reaction A+AA+B is studied in general dimension. The asymptotic decay of the system is found to depend nontrivially upon the initial concentration of A particles for certain ranges of the diffusion constant, backward reaction rate, and total concentration of particles. This nonequilibrium behavior is due to the formation of clusters centered about the initial A particles. A perturbative analysis ind=1 shows that the transition to the nonequilibrium dynamics is sharp and is quite similar to another previously studied reaction A+AA. Ford>1, a scaling argument is presented which describes the dependence of the asymptotic decay on the initial concentration of A particles and the equilibrium concentration for large backward reaction rates. Monte Carlo data are shown which confirm the analytic work ind=1, 2, and 3.     

Coarse-grained molecular dynamics simulations of capillary evaporation of water confined in hydrophilic mesopores

Non-equilibrium molecular dynamics (MD) simulations were performed to investigate the capillary evaporation of water confined in hydrophilic mesopores. The electrostatics-based (ELBA) coarse-grained water model was employed to calculate the duration of the time-consuming capillary evaporation process. To evaluate the effect of hydrophilicity of mesopores on the capillary evaporation of water, three types of thin films with a cylindrical mesopore were modelled by tuning the interactions between water and wall atoms. Initially, the cylindrical mesopore was filled with water, and evaporation of the water into vacuum was simulated. The calculation results showed that when capillary evaporation occurred, the desorption rate of water was almost constant in a highly hydrophilic mesopore where a stable water layer was formed on the pore surface, whereas the rate decreased with time in a weakly hydrophilic mesopore where the water layer did not remain stable. As time progressed, the water column shortened and then broke up. The number of water molecules in the mesopores decreased exponentially with time. The difference in the hydrophilicity of the mesopores resulted in different relaxation curves of water desorption from the mesopores.     

Thermodynamic properties of noble metal clusters:molecular dynamics simulation

The thermodynamics properties of noble metal clusters Au_N, Ag_N, Cu_N, and Pt_N (N = 80, 106, 140, 180, 216, 256, 312, 360, 408, 500, 628, 736, and 864) are simulated by micro-canonical molecular dynamics simulation technique. The potential energy and heat capacities change with temperature are obtained. The results reveal that the phase transition temperature of big noble metal clusters (N ⩾ 312 for Au, 180 for Ag and Cu, and 360 for Pt) increases linearly with the atom number slowly and approaches gently to bulk crystals. This phenomenon indicates that clusters are intermediate between single atoms and molecules and bulk crystals. But for the small noble clusters, the phase transition temperature changes irregularly with the atom number due to surface effect. All noble metal clusters have negative heat capacity around the solid-liquid phase transition temperature, and hysteresis in the melting/freezing circle is derived in noble metal clusters.     

Relaxation dynamics and power spectra of liquid water: a molecular dynamics simulation study

We present molecular dynamics simulations of liquid water at normal and supercooled conditions. Autocorrelation functions (ACFs) of several structural quantities and their fourier transforms are obtained and analysed. Structural correlations and relaxation times increase linearly with degree of supercooling. Power spectra of ACFs show increase in librational motion of liquid water with cooling. These modes intensify with supercooling because of structuring and ordering of water molecules. Overall, liquid water structure is homogenous over the temperatures and pressures studied and undergoes fluctuation–dissipation in its local-density variations [English and Tse, Phys. Rev. Lett. 106, 037801 (2011)].     

Thermal conductivity and thermal rectification in carbon nanotubes with geometric variations of doped nitrogen: Non-equilibrium molecular dynamics simulations

The thermal conductivity of carbon nanotubes with geometric variations of doped nitrogen is investigated. The phenomenon of thermal rectification shows that the heat transport is preferably in one direction. The asymmetric heat transport of the triangular single-nitrogen-doped carbon nanotubes (SNDCNTs) is larger than that of the parallel various-nitrogen-doped carbon nanotubes (VNDCNTs).     

Quantum molecular dynamics approach to estimate spallation yield from<Emphasis Type="Italic">p</Emphasis> +<Superscript>208</Superscript>Pb reaction at 800 MeV

The spallation yield of neutrons and other mass fragments produced in 800 MeV proton induced reaction on²⁰⁸Pb have been calculated in the framework of quantum molecular dynamics (QMD) model. The energy spectra and angular distribution have been calculated. Also, multiplicity distributions of the emitted neutrons and kinetic energy carried away by them have been estimated and compared with the available experimental data. The agreement is satisfactory. A major contribution to the neutron emission comes from statistical decay of the fragments. For mass and charge distributions of spallation products the QMD process gives rise to target-like and projectile-like fragments only.     

Large-scale molecular dynamics simulations of high energy cluster impact on diamond surface

Large-scale molecular dynamics simulations with high acceleration energy on a diamond surface were performed in order to investigate the surface erosion process. Accelerated argon or CO₂ clusters (∼960 atoms, 100 keV/cluster) impacted on the (111) surface of diamond which consisted of more than 1,000,000 carbon atoms. A typical hemispherical crater appeared about 0.7 ps after the impact, and two or three-layered shockwaves were formed and propagated to certain directions, but the crater was immediately filled up with the fluidized hot carbon material due to the collective elastic recovery before the reflection of the shockwave. The impact energy of the cluster was at first transferred mainly as kinetic energy of the diamond surface in a short time, and the potential energy was activated later. The activated carbon and oxygen atoms from the impact cluster stimulated the evaporation from the diamond surface for the CO₂ cluster impact while the evaporation seemed to be suppressed by the argon atoms themselves for the argon cluster impact. Received 22 November 2000     

Thermal transport properties of defective graphene:A molecular dynamics investigation

In this work the thermal transport properties of graphene nanoribbons with randomly distributed vacancy defects are investigated by the reverse non-equilibrium molecular dynamics method. We find that the thermal conductivity of the graphene nanoribbons decreases as the defect coverage increases and is saturated in a high defect ratio range. Further analysis reveals a strong mismatch in the phonon spectrum between the unsaturated carbon atoms in 2-fold coordination around the defects and the saturated carbon atoms in 3-fold coordination, which induces high interfacial thermal resistance in defective graphene and suppresses the thermal conductivity. The defects induce a complicated bonding transform from sp2 to hybrid sp–sp2network and trigger vibration mode density redistribution, by which the phonon spectrum conversion and strong phonon scattering at defect sites are explained. These results shed new light on the understanding of the thermal transport behavior of graphene-based nanomaterials with new structural configurations and pave the way for future designs of thermal management phononic devices.     

Electroless formation of silver nanoaggregates: an experimental and molecular dynamics approach

The ability to manipulate matter to create non-conventional structures is one of the key issues of material science. The understanding of assembling mechanism at the nanoscale allows us to engineer new nanomaterials, with physical properties intimately depending on their structure.

This paper describes new strategies to obtain and characterise metal nanostructures via the combination of a top-down method, such as electron beam lithography, and a bottom-up technique, such as the chemical electroless deposition. We realised silver nanoparticle aggregates within well-defined patterned holes created by electron beam lithography on silicon substrates. The quality characteristics of the nanoaggregates were verified by using scanning electron microscopy and atomic force microscopy imaging. Moreover, we compared the experimental findings to molecular dynamics simulations of nanoparticles growth. We observed a very high dependence of the structure characteristics on the pattern nanowell aspect ratio. We found that high-quality metal nanostructures may be obtained in patterns with well aspect ratio close to one, corresponding to a maximum diameter of 50 nm, a limit above which the fabricated structures become less regular and discontinuous. When regular shapes and sizes are necessary, as in nanophotonics, these results suggest the pattern characteristics to obtain isolated, uniform and reproducible metal nanospheres.     

Structure of liquid bismuth calculated from pseudo-potentials and molecular dynamics

Earlier calculations on liquid bismuth have been done by using five conduction electrons. However, this metal presents, in the liquid state, a gap in its electronic density of states that clearly separates the s and the p bands. Thus, the number of free electrons to be considered is affected by the existence of the gap. Previous calculations on the structure of liquid bismuth with five conduction electrons did not give satisfactory results. Molecular dynamics calculations using an effective potential derived from the empty core potential (ECP) and from the local optimised model potential (OMP) are presented and compared with the results obtained with three (p) and five (s + p) conduction electrons. The results, obtained for the first time to our knowledge for liquid bismuth at different temperatures, with three conduction electrons and OMP are in very good agreement with the Waseda structural experimental data. This approach using three conduction electrons is confirmed by resistivity calculations using the t-matrix model.     

Lorentz gas shear viscosity via nonequilibrium molecular dynamics and Boltzmann's equation

When nonequilibrium molecular dynamics is used to impose isothermal shear on a two-body periodic system of hard disks or spheres, the equations of motion reduce to those describing a Lorentz gas under shear. In this shearing Lorentz gas a single particle moves, isothermally, through a spatially periodic shearing crystal of infinitely massive scatterers. The curvilinear trajectories are calculated analytically and used to measure the dilute Lorentz gas viscosity at several strain rates. Simulations and solutions of Boltzmann's equation exhibit shear thinning resembling that found inN-body nonequilibrium simulations. For the three-dimensional Lorentz gas we obtained an exact expression for the viscosity which is valid at all strain rates. In two dimensions this is not possible due to the anisotropy of the scattering.     

Manipulation of biomolecules: A molecular dynamics study

With the rapid progression of bionanorobotics, manipulation of nano-scale biosamples is becoming increasingly attractive for different biological purposes. Nevertheless, the interaction between a robotic probe and a biological sample is poorly understood and the conditions for appropriate handling is not well-known. Here, we use the molecular dynamics (MD) simulation method to investigate the manipulation process when a nanoprobe tries to move a biosample on a substrate. For this purpose, we have used Ubiquitin (UBQ) as the biomolecule, a single-walled carbon nanotube (SWCNT) as the manipulation probe, and a double-layered graphene sheets as the substrate. A series of simulations were conducted to study the effects of different conditions on the success of the manipulation process. These conditions include the tip diameter, the vertical gap between the tip and substrate, and the initial orientation of the protein. Also we have studied two strategies for the manipulation of the protein by a nano-scale probe that we have named pushing and pulling. Interaction force between carbon nanotube (CNT) tips and the biomolecule, the root-mean-square deviation (RMSD), and the radius of gyration of the protein are monitored for different conditions. We found that larger tip diameters, smaller gaps between tip and substrate, and a pulling strategy increase the chance of a successful manipulation.     

Visualization of chemical reaction dynamics: Toward understanding complex polyatomic reactions

Polyatomic molecules have several electronic states that have similar energies. Consequently, their chemical dynamics often involve nonadiabatic transitions between multiple potential energy surfaces. Elucidating the complex reactions of polyatomic molecules is one of the most important tasks of theoretical and experimental studies of chemical dynamics. This paper describes our recent experimental studies of the multidimensional multisurface dynamics of polyatomic molecules based on two-dimensional ion/electron imaging. It also discusses ultrafast photoelectron spectroscopy of liquids for elucidating nonadiabatic electronic dynamics in aqueous solutions.     

Predicting XAFS scattering path cumulants and XAFS spectra for metals (Cu,Ni, Fe,Ti, Au) using molecular dynamics simulations

The ability of molecular dynamics (MD) simulations to support the analysis of X‐ray absorption fine‐structure (XAFS) data for metals is evaluated. The low‐order cumulants (ΔR, σ², C₃) for XAFS scattering paths are calculated for the metals Cu, Ni, Fe, Ti and Au at 300 K using 28 interatomic potentials of the embedded‐atom method type. The MD cumulant predictions were evaluated within a cumulant expansion XAFS fitting model, using global (path‐independent) scaling factors. Direct simulations of the corresponding XAFS spectra, χ(R), are also performed using MD configurational data in combination with the FEFFab initio code. The cumulant scaling parameters compensate for differences between the real and effective scattering path distributions, and for any errors that might exist in the MD predictions and in the experimental data. The fitted value of ΔR is susceptible to experimental errors and inadvertent lattice thermal expansion in the simulation crystallites. The unadjusted predictions of σ² vary in accuracy, but do not show a consistent bias for any metal except Au, for which all potentials overestimate σ². The unadjusted C₃ predictions produced by different potentials display only order‐of‐magnitude consistency. The accuracy of direct simulations of χ(R) for a given metal varies among the different potentials. For each of the metals Cu, Ni, Fe and Ti, one or more of the tested potentials was found to provide a reasonable simulation of χ(R). However, none of the potentials tested for Au was sufficiently accurate for this purpose.