Yuta Yoshimoto

Construction of non-Markovian coarse-grained models employing the Mori–Zwanzig formalism and iterative Boltzmann inversion

We propose a new coarse-grained (CG) molecular simulation technique based on the Mori-Zwanzig (MZ) formalism along with the iterative Boltzmann inversion (IBI). Non-Markovian dissipative particle dynamics (NMDPD) taking into account memory effects is derived in a pairwise interaction form from the MZ-guided generalized Langevin equation. It is based on the introduction of auxiliary variables that allow for the replacement of a non-Markovian equation with a Markovian one in a higher dimensional space. We demonstrate that the NMDPD model exploiting MZ-guided memory kernels can successfully reproduce the dynamic properties such as the mean square displacement and velocity autocorrelation function of a Lennard-Jones system, as long as the memory kernels are appropriately evaluated based on the Volterra integral equation using the force-velocity and velocity-velocity correlations. Furthermore, we find that the IBI correction of a pair CG potential significantly improves the representation of static properties characterized by a radial distribution function and pressure, while it has little influence on the dynamic processes. Our findings suggest that combining the advantages of both the MZ formalism and IBI leads to an accurate representation of both the static and dynamic properties of microscopic systems that exhibit non-Markovian behavior.

Incident energy dependence of scattering behavior of water molecules on Si (100) and graphite surfaces

The interaction between water molecules and solid surfaces has a great impact on water vapor flows in nanostructures. We conduct molecular beam scattering experiments covering the incident energy range corresponding to the thermal energy at room temperature to investigate the scattering behavior of water molecules on silicon and graphite surfaces. The incident energy dependence of the scattering distributions exhibits opposite trends on these surfaces. Molecular dynamics simulations reveal that the difference is caused by the inertia effect of the incident molecules and the surface corrugations.

A non-diaphragm type small shock tube for application to a molecular beam source.

A non-diaphragm type small shock tube was developed for application to a molecular beam source, which can generate beams in the energy range from 1 to several electron volts and beams containing dissociated species such as atomic oxygen. Since repetitive high-frequency operation is indispensable for rapid signal acquisition in beam scattering experiments, the dimensions of the shock tube were miniaturized to reduce the evacuation time between shots. The designed shock tube is 2-4 mm in diameter and can operate at 0.5 Hz. Moreover, a high shock Mach number at the tube end is required for high-energy molecular beam generation. To reduce the shock attenuation caused by the wall boundary layer, which becomes significant in small-diameter tubes, we developed a high-speed response valve employing the current-loop mechanism. The response time of this mechanism is about 100 μs, which is shorter than the rupture time of conventional diaphragms. We show that the current-loop valve generates shock waves with shorter formation distances (about 200-300 mm) than those of conventional shock tubes. In addition, the converging geometry efficiently accelerates shock wave in the small-diameter tubes. The optimal geometry of the shock tube yields shock Mach number around 7, which indicates that the translation energy of molecular beams can exceed 1 eV even in the presence of the real gas effect.

Mutual influence of molecular diffusion in gas and surface phases

We develop molecular transport simulation methods that simultaneously deal with gas- and surface-phase diffusions to determine the effect of surface diffusion on the overall diffusion coefficients. The phenomenon of surface diffusion is incorporated into the test particle method and the mean square displacement method, which are typically employed only for gas-phase transport. It is found that for a simple cylindrical pore, the diffusion coefficients in the presence of surface diffusion calculated by these two methods show good agreement. We also confirm that both methods reproduce the analytical solution. Then, the diffusion coefficients for ink-bottle-shaped pores are calculated using the developed method. Our results show that surface diffusion assists molecular transport in the gas phase. Moreover, the surface tortuosity factor, which is known to be uniquely determined by physical structure, is influenced by the presence of gas-phase diffusion. This mutual influence of gas-phase diffusion and surface diffusion indicates that their simultaneous calculation is necessary for an accurate evaluation of the diffusion coefficients.

Effect of capillary condensation on gas transport properties in porous media

We investigate the effect of capillary condensation on gas diffusivity in porous media composed of randomly packed spheres with moderate wettability. To simulate capillary phenomena at the pore scale while retaining complex pore networks of the porous media, we employ density functional theory (DFT) for coarse-grained lattice gas models. The lattice DFT simulations reveal that capillary condensations preferentially occur at confined pores surrounded by solid walls, leading to the occlusion of narrow pores. Consequently, the characteristic lengths of the partially wet structures are larger than those of the corresponding dry structures with the same porosities. Subsequent gas diffusion simulations exploiting the mean-square displacement method indicate that while the effective diffusion coefficients significantly decrease in the presence of partially condensed liquids, they are larger than those in the dry structures with the same porosities. Moreover, we find that the ratio of the porosity to the tortuosity factor, which is a crucial parameter that determines an effective diffusion coefficient, can be reasonably related to the porosity even for the partially wet porous media.

Hyperthermal molecular beam source using a non-diaphragm-type small shock tube

We have developed a hyperthermal molecular beam source employing a non-diaphragm-type small shock tube for gas-surface interaction studies. Unlike conventional shock-heated beam sources, the capability of repetitive beam generation without the need for replacing a diaphragm makes our beam source suitable for scattering experiments, which require signal accumulation for a large number of beam pulses. The short duration of shock heating alleviates the usual temperature limit due to the nozzle material, enabling the generation of a molecular beam with higher translational energy or that containing dissociated species. The shock-heated beam is substantially free from surface-contaminating impurities that are pronounced in arc-heated beams. We characterize the properties of nitrogen and oxygen molecular beams using the time-of-flight method. When both the timing of beam extraction and the supply quantity of nitrogen gas are appropriately regulated, our beam source can generate a nitrogen molecular beam with translational energy of approximately 1 eV, which corresponds to the typical activation energy of surface reactions. Furthermore, our beam source can generate an oxygen molecular beam containing dissociated oxygen atoms, which can be a useful probe for surface oxidation. The dissociation fraction along with the translational energy can be adjusted through the supply quantity of oxygen gas.

High-Energy Molecular Beam Source Using a Non-diaphragm Type Small Shock Tube

The molecular beam technique [1] is one of the powerful tools to analyze gassurface interactions. Various methods have been developed to generate the molecular beams with the translational energy of 1-several eV, which corresponds to the typical activation energy of surface reactions. Although seeded beams combined with a heated nozzle are often used, the heatproof temperature of the nozzle limits the beam energy.Arc-heated beams [2] have the energy ofmore than 1 eV. The problem is, however, that the beams contain copper atoms due to electrode erosion and thus contaminate surfaces. Several researchers also investigated shock-heated beam sources [3]. The replacement of a diaphragm and the long evacuation time between each shot, however, make the conventional shock-heated beam sources impractical for the scattering experiments of gas molecules on surfaces, since the scattering experiments require signal accumulation for a large number of beam pulses. In order to overcome these shortcomings, we have been developing a beam source using a nondiaphragm type small shock tube [4]. Our objective is to develop a shock-heated beam source which can generate the beams with the translational energy of more than 1 eV with high operating frequency. It is noteworthy that the inner diameter of our shock tube is a few millimeters, far smaller than that of conventional shock tubes. The volume reduction leads to the shorter evacuation time, which enables generating molecular beams with high operating frequency. On the other hand, it should be noted that the boundary layer has significant effects on shock propagation in small diameter tubes [5]. In addition, we developed a high-speed valve employing a current-loop mechanism [4] as a substitute for a diaphragm to reduce shock formation distance, which determines the tube length.

Measurements of time-of-flight distributions of shock-heated molecular beams

Molecular beam source employing a shock tube is an attractive choice for the translational energy of around 1 eV, which corresponds to the typical activation energy of surface reactions. We developed a non-diaphragm type small shock tube as the molecular beam source generating high energy and dissociated molecular beams. The drastic reduction of the tube volume enables the repetitive operation of the shock tube at the frequency of 0.5 Hz. Installing the shock tube into the molecular beam setup, we measured the time-of-flight distributions of nitrogen and oxygen beams, and demonstrated the performance on controllability of the beam energy and the dissociation rate of molecules.

High‐Energy Molecular Beam Source Using a Small Shock Tube: Evaluation of Convergent Type Design

Molecular beam source using a small shock tube has the potential to frequently generate high energy molecular beam in a range of 1–5 eV without any undesirable impurities. We measured shock Mach numbers in 2 and 4‐mm‐diameter straight tubes to know about the propagation of shock wave in a very small shock tube. In addition, we measured shock Mach numbers in convergent shock tubes of which diameters linearly decrease from 4 mm to 2 mm, which demonstrated the possibility of a convergent shock tube to generate higher energy molecular beam than straight one.