Alessio Alexiadis

Molecular Simulation of Water in Carbon Nanotubes

7.1. Water Structure in Carbon Nanotubes 5020 7.2. Radial, Axial, and Total Water Density 5023 7.3. Hydrogen Bonds 5024 7.4. Filling Carbon Nanotubes with Water 5025 7.5. Dipole Moment 5026 7.6. Proton Transport in Water 5027 7.7. Transport Properties 5027 8. Driven Flow 5029 9. Charged Carbon Nanotubes 5029 10. Polarizable Carbon Nanotubes 5030 11. Selective Partitioning 5030 12. Functionalized Carbon Nanotubes 5031 13. Conclusions 5031 14. Acknowledgments 5031 15. References 5031

The Discrete Multi-Hybrid System for the Simulation of Solid-Liquid Flows

This study proposes a model based on the combination of Smoothed Particle Hydrodynamics, Coarse Grained Molecular Dynamics and the Discrete Element Method for the simulation of dispersed solid-liquid flows. The model can deal with a large variety of particle types (non-spherical, elastic, breakable, melting, solidifying, swelling), flow conditions (confined, free-surface, microscopic), and scales (from microns to meters). Various examples, ranging from biological fluids to lava flows, are simulated and discussed. In all cases, the model captures the most important features of the flow.

Using discrete multi-physics for detailed exploration of hydrodynamics in an in vitro colon system

We developed a mathematical model that describes the motion of viscous fluids in the partially-filled colon caused by the periodic contractions of flexible walls (peristalsis). In-vitro data are used to validate the model. The model is then used to identify two fundamental mechanisms of mass transport: the surfing mode and the pouring mode. The first mechanism is faster, but only involves the surface of the liquid. The second mechanism causes deeper mixing, and appears to be the main transport mechanism. Based on the gained understanding, we propose a series of measures that can improve the reliability of in-vitro models. The tracer in PET-like experiments, in particular, should not be injected in the first pocket, and its viscosity should be as close as possible to that of the fluid. If these conditions are not met, the dynamics of the tracer and the fluid diverge, compromising the accuracy of the in-vitro data.

Discrete multi-physics: A mesh-free model of blood flow in flexible biological valve including solid aggregate formation

We propose a mesh-free and discrete (particle-based) multi-physics approach for modelling the hydrodynamics in flexible biological valves. In the first part of this study, the method is successfully validated against both traditional modelling techniques and experimental data. In the second part, it is further developed to account for the formation of solid aggregates in the flow and at the membrane surface. Simulations of various types of aggregates highlight the main benefits of discrete multi-physics and indicate the potential of this approach for coupling the hydrodynamics with phenomena such as clotting and calcification in biological valves.

Modelling and simulation of flow and agglomeration in deep veins valves using discrete multi physics

The hemodynamics in flexible deep veins valves is modelled by means of discrete multi-physics and an agglomeration algorithm is implemented to account for blood accrual in the flow. Computer simulations of a number of valves typologies are carried out. The results show that the rigidity and the length of the valve leaflets play a crucial role on both mechanical stress and stagnation in the flow. Rigid and short membranes may be inefficient in preventing blood reflux, but reduce the volume of stagnant blood potentially lowering the chances of thrombosis. Additionally, we also show that in venous valves, cell agglomeration is driven by stagnation rather than mechanical stress.

A Particle-Continuum Hybrid Framework for Transport Phenomena and Chemical Reactions in Multicomponent Systems at the Micro and Nanoscale

The particle-continuum hybrid Laplacian method is extended as a framework for modeling all transport phenomena in fluids at the micro and nanoscale including multicomponent mass transfer and chemical reactions. The method is explained, and the micro-to-macro and macro-to-micro coupling steps are discussed. Two techniques for noise reduction (namely, the bonsai box (BB) and the seamless strategy) are discussed. Comparisons with benchmark full-molecular dynamics (MD) cases for micro and nano thermal and reacting flows show excellent agreement and good computational efficiency.

Discrete multi-physics simulations of diffusive and convective mass transfer in boundary layers containing motile cilia in lungs

In this paper, the mass transfer coefficient (permeability) of boundary layers containing motile cilia is investigated by means of discrete multi-physics. The idea is to understand the main mechanisms of mass transport occurring in a ciliated-layer; one specific application being inhaled drugs in the respiratory epithelium. The effect of drug diffusivity, cilia beat frequency and cilia flexibility is studied. Our results show the existence of three mass transfer regimes. A low frequency regime, which we called shielding regime, where the presence of the cilia hinders mass transport; an intermediate frequency regime, which we have called diffusive regime, where diffusion is the controlling mechanism; and a high frequency regime, which we have called convective regime, where the degree of bending of the cilia seems to be the most important factor controlling mass transfer in the ciliated-layer. Since the flexibility of the cilia and the frequency of the beat changes with age and health conditions, the knowledge of these three regimes allows prediction of how mass transfer varies with these factors.

Temperature and configurational effects on the Young’s modulus of poly (methyl methacrylate): a molecular dynamics study comparing the DREIDING, AMBER and OPLS force fields

Abstract The effects of the configuration and temperature on the Young’s modulus of poly (methyl methacrylate) (PMMA) have been studied using molecular dynamics simulations. For the DREIDING force field under ambient temperatures, increasing the number of monomers significantly increases the modulus of isotactic and syndiotactic PMMA while the isotactic form has a greater modulus. The effects of temperature on the modulus of isotactic PMMA have been simulated using the DREIDING, AMBER, and OPLS force fields. All these force fields predict the effects of temperature on the modulus from 200 to 350 K that are in close agreement with experimental values, while at higher temperatures the moduli are greater than those measured. The glass transition temperature determined by the force fields, based on the variation of the modulus with temperature, is greater than the experimental values, but when obtained from a plot of the volume as a function of the temperature, there is closer agreement. The Young’s moduli calculated in this study are in closer agreement to the experimental data than those reported by previous simulations.