Bridging large and small scales of water models using hybrid Molecular Dynamics/Fluctuating Hydrodynamics framework

This thesis presents a two-dimensional water model investigation and development of a multiscale method for the modelling of large systems, such as virus in water or peptide immersed in the solvent. We have implemented a two-dimensional ‘Mercedes Benz’ (MB) or BN2D water model using Molecular Dynamics. We have studied its dynamical and structural properties dependence on the model’s parameters. For the first time we derived formulas to calculate thermodynamic properties of the MB model in the microcanonical (NVE) ensemble. We also derived equations of motion in the isothermal–isobaric (NPT) ensemble. We have analysed the rotational degree of freedom of the model in both ensembles. We have developed and implemented a self-consistent multiscale method, which is able to communicate micro- and macro- scales. This multiscale method assumes, that matter consists of the two phases. One phase is related to micro- and the other to macroscale. We simulate the macro scale using Landau Lifshitz-Fluctuating Hydrodynamics, while we describe the microscale using Molecular Dynamics. We have demonstrated that the communication between the disparate scales is possible without introduction of fictitious interface or approximations which reduce the accuracy of the information exchange between the scales. We have investigated control parameters, which were introduced to control the contribution of each phases to the matter behaviour. We have shown, that microscales inherit dynamical properties of the macroscales and vice versa, depending on the concentration of each phase. We have shown, that Radial Distribution Function is not altered and velocity autocorrelation functions are gradually transformed, from Molecular Dynamics to Fluctuating Hydrodynamics description, when phase balance is changed. In this work we test our multiscale method for the liquid argon, BN2D and SPC/E water models. For the SPC/E water model we investigate microscale fluctuations which are computed using advanced mapping technique of the small scales to the large scales, which was developed by Voulgarakisand et. al.

Complexity of classical dynamics of molecular systems. II. Finite statistical complexity of a water-Na+ system

The computational mechanics approach has been applied to the orientational behavior of water molecules in a molecular dynamics simulated water–Na + system. The distinctively different statistical complexity of water molecules in the bulk and in the first solvation shell of the ion is demonstrated. It is shown that the molecules undergo more complex orientational motion when surrounded by other water molecules compared to those constrained by the electric field of the ion. However the spatial coordinates of the oxygen atom shows the opposite complexity behavior in that complexity is higher for the solvation shell molecules. New information about the dynamics of water molecules in the solvation shell is provided that is additional to that given by traditional methods of analysis.

Polymer optical fiber grating as water activity sensor

Controlling the water content within a product has long been required in the chemical processing, agriculture, food storage, paper manufacturing, semiconductor, pharmaceutical and fuel industries. The limitations of water content measurement as an indicator of safety and quality are attributed to differences in the strength with which water associates with other components in the product. Water activity indicates how tightly water is "bound," structurally or chemically, in products. Water absorption introduces changes in the volume and refractive index of poly(methyl methacrylate) PMMA. Therefore for a grating made in PMMA based optical fiber, its wavelength is an indicator of water absorption and PMMA thus can be used as a water activity sensor. In this work we have investigated the performance of a PMMA based optical fiber grating as a water activity sensor in sugar solution, saline solution and Jet A-1 aviation fuel. Samples of sugar solution with sugar concentration from 0 to 8%, saline solution with concentration from 0 to 22%, and dried (10ppm), ambient (39ppm) and wet (68ppm) aviation fuels were used in experiments. The corresponding water activities are measured as 1.0 to 0.99 for sugar solution, 1.0 to 0.86 for saline solution, and 0.15, 0.57 and 1.0 for the aviation fuel samples. The water content in the measured samples ranges from 100% (pure water) to 10 ppm (dried aviation fuel). The PMMA based optical fiber grating exhibits good sensitivity and consistent response, and Bragg wavelength shifts as large as 3.4 nm when the sensor is transferred from dry fuel to wet fuel. © 2014 Copyright SPIE.

Molecular Dynamics implementation of BN2D or 'Mercedes Benz' water model

Two-dimensional 'Mercedes Benz' (MB) or BN2D water model (Naim, 1971) is implemented in Molecular Dynamics. It is known that the MB model can capture abnormal properties of real water (high heat capacity, minima of pressure and isothermal compressibility, negative thermal expansion coefficient) (Silverstein et al., 1998). In this work formulas for calculating the thermodynamic, structural and dynamic properties in microcanonical (NVE) and isothermal-isobaric (NPT) ensembles for the model from Molecular Dynamics simulation are derived and verified against known Monte Carlo results. The convergence of the thermodynamic properties and the system's numerical stability are investigated. The results qualitatively reproduce the peculiarities of real water making the model a visually convenient tool that also requires less computational resources, thus allowing simulations of large (hydrodynamic scale) molecular systems. We provide the open source code written in C/C++ for the BN2D water model implementation using Molecular Dynamics.

Multiscale molecular dynamics/hydrodynamics implementation of two dimensional “Mercedes Benz” water model

A multiscale Molecular Dynamics/Hydrodynamics implementation of the 2D Mercedes Benz (MB or BN2D) [1] water model is developed and investigated. The concept and the governing equations of multiscale coupling together with the results of the two-way coupling implementation are reported. The sensitivity of the multiscale model for obtaining macroscopic and microscopic parameters of the system, such as macroscopic density and velocity fluctuations, radial distribution and velocity autocorrelation functions of MB particles, is evaluated. Critical issues for extending the current model to large systems are discussed.

Polarization dynamics of dissipative solitons in a erbium doped fiber laser passively mode locked by carbon nanotube polymer composite

Here we present first investigation of polarization dynamics from a carbon nanotube mode locked erbium doped fiber laser. Both vector and polarization switching dissipative soliton have been observed. © 2014 Optical Society of America.

Improving the response time of polymer optical fibre Bragg grating water activity sensors

In this work we investigate the effect of temperature and diameter size on the response time of a poly(methyl methacrylate) based, polymer optical fibre Bragg grating water activity sensor. The unstrained and etched sensor was placed in an environmental chamber to maintain controlled temperature and humidity conditions and subjected to step changes in humidity. The data show a strong correlation between decrease in diameter and shorter response time. A decrease in response time was also observed with an increase in temperature.