Thien Tran-Duc

Modelling the interaction in a benzene dimer

The interaction between aromatic rings is a fundamental problem in material science and biochemistry. These interactions are generally found to stabilise protein molecules and the double helical structure of DNA, and they also play an important role in the recognition processes in biological and non-biological systems. However, the complexity and variety in the structures and components of aromatic compounds are major obstacles to investigating their interactions. In this study, the simplest case of aromatic interactions, which is the interaction between two benzene rings, is modelled using a continuous approximation. Assuming a constant atomic surface density and modelling the structure of a benzene molecule as a combination of two rings, namely an inner carbon ring and an outer hydrogen ring, the van der Waals interaction between any two benzene rings can be obtained as the sum of four interactions. The major result obtained here is an analytical expression for the potential energy which can then be used to predict equilibrium configurations for two interacting benzene molecules. Moreover, we find that at sufficiently large distances between the two benzene molecules, the orientational angle φ at which the interaction energy is a minimum can be approximated by the arctan of the ratio of two separation distances in two mutually perpendicular directions.

A smoothed particle hydrodynamics (SPH) study of sediment dispersion on the seafloor

Ocean-scale sediment dispersion and sedimentation problems are studied using the Smoothed Particle Hydrodynamics (SPH). A SPH formulation based on a mixture model for two-phase flows is developed to investigate the problem. The sediment mass transport via the settling advection and the turbulent diffusion of the suspended sediment are fully accounted for in the current SPH model. The simulations are carried out in an opened boundary domain with a unidirectional underlined current, with relevant deposition/re-suspension boundary conditions on the seafloor. The factors influencing the sedimentation process, such as the hindering and the bottom shear stress effects, are also considered. The simulation results reveal that the sediment convection near the sediment source location is caused by both the ocean current and secondary density driven flows that are created by the concurrent settling motion of suspended sediment particles, while the downstream sediment transport in the far field is only driven by the ...

Modeling encapsulation of acetylene molecules into carbon nanotubes

Polyacetylene is a well-known conductive polymer and when doped its conductivity can be altered by up to 12 orders of magnitude. However, due to entropy effects a polyacetylene chain usually suffers from distortions and interchain couplings which lead to unpredictable changes in its conducting property. Encapsulating a polyacetylene chain into a carbon nanotube can resolve these issues. Furthermore, since the carbon nanotube itself possesses excellent electrical conductivity, the combination of the carbon nanotube and polyacetylene may give rise to a new material with superior transport behavior. In this paper, we model mathematically the molecular interaction between an acetylene molecule and a carbon nanotube in order to determine conditions at which configurations of the acetylene molecule are accepted into the carbon nanotube as well as its equilibrium configurations inside various sizes of carbon nanotubes. For special cases of the acetylene molecule lying on the tube axis, standing vertically with its center on the tube axis and staying far inside the tube, explicit analytical expressions for the interaction energy are obtained.

Rheology of bubble suspensions using dissipative particle dynamics. Part I: A hard-core DPD particle model for gas bubbles

In this paper, the rheology of dilute bubble suspensions is studied using dissipative particle dynamics (DPD). Each gas bubble is modeled by a hard-core DPD particle. The approach addresses the issue of zero-viscosity arising from modeling of a gas bubble by a set of DPD particles. Moreover, it helps to reduce significantly the computational demand due to a much less number of DPD particles required in the simulation. A dissipative layer is created outside the effective region of the hard-core DPD particle to manage the hydrodynamic force acting on it, and different phases can be defined accordingly. The model is further examined in the simulation of dilute bubble suspensions, and measurements on the Newtonian viscosity for the volume fraction less than 15% are consistent with experimental results and results from theoretical models in continuum mechanics at low Ca limit.

General Model for Molecular Interactions in a Benzene Dimer

Modelling molecular interactions in a benzene dimer is a typical example of a class of problems involving aromatic molecules. Although many studies on the benzene dimer have been carried out both theoretically and experimentally and energetically favorable structures of a benzene dimer have been found, an investigation of all equilibrium structures of a benzene dimer has not so far been done. Previously, the present authors investigated the interaction energy and geometries of a benzene dimer for the special case in which only one rotational angle is used to describe the relative position between two benzene molecules. In general, two rotational angles are necessary to describe the most general relative orientation. Here, we apply the same approach in which the discrete atomic structure of a benzene molecule is replaced by two continuous rings of atoms, namely an inner carbon ring and an outer hydrogen ring with average constant atomic densities and the molecular interaction forces are calculated from the Lennard-Jones potential function. An analytical expression for the interaction energy is obtained which we use to determine all equilibrium structures of a benzene dimer as well as to determine those domains in which certain configurations are more favorable than others. Our results show that parallel, T-shaped, parallel displaced and tilted structures are all possible configurations of a benzene dimer and they exist at different regions of vertical and offset distances at different energy levels.

A smoothed particle hydrodynamics (SPH) study on polydisperse sediment from technical activities on seabed

Technical activities to collect poly-metallic nodules on a seabed are likely to disturb the top-layer sediment and re-suspend it into the ambient ocean water. The transport of the re-suspended polydisperse-sized sediment is a process in which particles’ size variation leads to a difference in their settling velocities; and thus the polydispersity in sizes of sediment has to be taken into account in the modeling process. The sediment transport within a window of 12 km is simulated and analyzed numerically in this study. The sediment characteristic and the ocean current data taken from the Peru Basin, Pacific Ocean, are used in the simulations. More than 50% of the re-suspended sediment are found to return to the bottom after 24 h. The sediment concentration in the ambient ocean water does not exceed 3.5 kg/m3 during the observed period. The deposition rate steadily increases and reaches 70% of the sediment re-suspension rate after 24 h. The sediment plume created by the activities comprises mainly very fin...

Modelling interactions between a PBB and fullerenes

Fullerenes have many uses including in medical and electronic nanodevices. High pressure liquid chromatography (HPLC) columns are generally used to extract a certain structure of fullerne from a mixture of them. In this paper, we investigate the interactions between various types of fullerenes and a station phase in HPLC known as pentabromobenzyl (PBB). The Lennard-Jones potential and a continuum approach are employed to determine the van der Waals energy of these interactions within the HPLC columns. The equilibrium configurations for any given distance between a fullerene and the centre of a PBB are obtained. Results of this study may assist the design of a chromatography column for fullerene separation.

Sediment transport over seabed with Smoothed Particle Hydrodynamics

A lab-scaled sediment transport over seabed is investigated. The sediment flow in sea water is modelled as flow of a yield stress fluid (sediment) in a Newtonian fluid (sea water). Papanastasiou model is utilized to calculate viscosity of the sediment with the yielding-time parameter set to10000s, corresponding to yielding occurrence at shear rate of 0.001s−1. The yield stress value of the sediment with 0.2 mass fraction of the solid phase is 2kPa, which is obtained from measurements carried out on sediment collected in the Clarion and Clipperton Fracture Zones in the Pacific Ocean.