Doctor of Philosophy in Chemical and Biological Engineering (PhD)
Molecular Dynamics simulation of piezo-ionic sensors
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We use a molecular dynamics (MD) framework to study the mechanical propertiesof triblock copolymer materials which form thermoplastic elastomers (TPEs). Thesematerials form physical, rather than chemical, cross-links as a result of their phaseseparatednano-structure. It is difficult, or impossible, to measure the details ofnetwork chains and monomers experimentally. However, it is these microscopicfeatures that give rise to the material’s elastomeric properties. We use a coarsegrainedbead-spring model which retains the vital details of the chain network andthe nano-structured regions while removing unnecessary atomistic detail.We first present a simulation strategy for the equilibration of nano-structuredcopolymer melt morphologies. MD simulations with a soft pair potential that allowsfor chain crossing result in efficient modelling of phase segregation. We successfullyreintroduce excluded volume pair interactions with only a short re-equilibration ofthe local structure, allowing configurations generated (with this method) to be usedfor studies of structural and mechanical properties.We then study the plastic deformation of triblock TPEs, probing the microscopicmechanisms operative during deformation and how they connect to the macroscopicstress response. We compare two deformation modes, uniaxial stress and strain,which emulate experimental tests and conditions around material failure. We findthat triblocks’ stress response exhibits a significant increase in strain hardeningcompared to homopolymeric chains. We analyse several microscopic properties,including: the chain deformation, monomer displacement, deformation and divisionof glassy domains, and void formation.We introduce an entropic network model for the stress response utilising microscopicinformation about chain configurations and their topological constrains.The model assumes additive contributions from chain stretch and the stretch betweenchain entanglement points and results in quantitative prediction of the stressresponse. Only one parameter fit is required to describe both triblock and homopolymerssystems. We compare our model to recent entropic models developedfor vulcanised rubbers and probe its limitations and more general applicability. Extensionsto more complicated architectures are possible (e.g. stars).
This thesis presents a computational study of the interaction between solute atoms and defects in the crystal lattice of metals at low solute concentrations. To accurately capture the electronic behaviour of these solutes in complex environments, we use density functional theory calculations. We begin by examining the diffusion of technologically relevant rare earth solutes in Mg. The calculated activation energies agree qualitatively with experimental values. This work also demonstrates that the existing 8-frequency model for diffusion in hexagonally close-packed metals can be improved with the consideration of an additional vacancy jump frequency. We calculate the binding energies of solute atoms to a Ʃ7 grain boundary in Mg. These energies are dominated by elastic effects for many important alloying species, and we develop a computationally efficient model for predicting the binding energies for these elastically dominated solutes. These results agree well with the findings of other experimental and computational studies of Mg boundaries. Using molecular statics calculations of general high-angle grain boundaries in combination with our binding energy model, we predict binding energies for boundaries not accessible by quantum calculations. In addition to providing a better understanding of solute-grain boundary interaction in Mg, binding energies for use in models at higher length scales, and a new, efficient model for predicting binding energy, we also show the importance of using segregation models which utilize multiple binding energies to predict segregation levels. We develop an improved multiscale method for embedding quantum mechanical density functional theory calculations in much larger classical simulations. This method removes the constraints on structure size usually imposed by the high cost of quantum calculations by treating a small region of interest (e.g. a solute and its neighbourhood) with quantum accuracy while coupling the quantum domain to a much larger classical system. The method is developed and tested using solute binding energies to a vacancy and to sites at a special, high-symmetry grain boundary in Al, for which purely quantum mechanical evaluations are also possible, providing a reliable benchmark. We then apply this method to find solute binding energy to a general, low-symmetry grain boundary in Al.
This thesis aims to understand the nanoscale effects of water as a structured solvent on the phenomenon of counterion-induced DNA condensation. We present results of molecular dynamics simulations of the electrostatic interaction between two DNA molecules in the presence of divalent counterions in different solvation models. We also develop a coarse-grained implicit solvent model for investigating the dynamics on long time and length scales. In the first project, we investigate the role of the solvation effects on the interaction between like-charged cylindrical rods as simplified model for DNA molecules. We obtain the average force between two parallel charged rods in simulations that differ only by their representation of water as a implicit or explicit solvent, but have otherwise identical parameters. We find that the presence of water molecules changes the structure of the counterions and results in both qualitative and quantitative changes of the force between highly charged polyelectrolytes. In the second project, we explore the importance of the DNA geometry on the electrostatic forces by considering two rigid helical models. The simulation results indicate that the DNA shape is an essential contributor to the interaction. A regime of attractive interaction, which disappeared in the cylindrical model, is recovered in the explicit solvent model in both types of helical models. The results also confirm that the behaviour of the interactions between two DNA molecules in the explicit solvent model are different from the implicit solvent models. In the third project, we develop a coarse-grained (CG) representation of these solvation effects. This CG model is constructed from explicit simulations and significantly reduces the computational expense. Short-ranged corrections are added to the pair-wise interaction potentials in the implicit solvent model such that the structure of counterions in the system is consistent with the results from the explicit solvent simulations. This CG model succeeds in reproducing the like-charge attraction effect between DNA molecules in explicit simulations.In a final project, we apply the CG model developed previously to study three DNA strands in the presence of divalent counterions as a starting point for investigating many-body effects in the mechanism of DNA bundling.
Microscopic dynamics and mechanical response of polymer glasses are studied in four projects using molecular dynamics simulations of a simple bead-spring model. The first project studies the interplay between physical aging and mechanical perturbation. Structural, dynamical and energetic quantities are monitored in the recovery regime following aging and uniaxial tensile deformation periods. The total engineering strain is found to control a continuous transition from transient to permanent mechanical rejuvenation: After deformation in the pre-yield regime all quantities quickly reset to pre-deformation values, while deformation around the yield point results in the erasure of aging history. Deformation in the post-yield regime, however, drives the system into a distinct thermodynamic state.In the second project, I introduce an efficient algorithm that detects microscopic relaxation events, which are the basis of aging dynamics and plasticity. I use this technique to calculate the density-density correlations from the spatio-temporal distribution of so called hops in quiescent polymer glasses at different temperatures and ages. Correlation ranges are extracted and I analyze the size distributions of collaboratively rearranging groups of particles. Furthermore, I spatially resolve dynamical heterogeneity (DH) as hop-clusters, and I compare cluster growth, as well as volume distribution during aging with the four-point dynamical susceptibility Χ₄ as the established measure of DH.The third and fourth project use the hop detection technique to investigate the link between relaxation events and local structure. Quasi-localized low-energy vibrational modes, called soft modes, are found to correlate with the location and direction of hops. In the third project, I analyze the temperature- and age-dependence of this correlation in quiescent polymer glasses, and I show that the soft modes are long lived structural features. The fourth project extends the analysis to mechanically deformed polymer glasses. I find that the spatial correlation of hops and soft modes is reduced to pre-aging values after deformation in the strain softening regime. This reveals an additional perspective on mechanical rejuvenation and substantiates the findings from the first project. In the strain hardening regime the correlation increases, and this novel effect is linked to a growing localization of the soft modes.
Non-equilibrium dynamics in the glassy state lead to interesting aging and memory effects. In this dissertation, extensive computer simulations are performed in order to determine the microscopic origin of these phenomena. Molecular dynamics simulations show all of the qualitative characteristics of real glasses and additionally provide microscopic information that is not typically available to experiments. After a rapid quench to the glassy state, particle correlation functions exhibit dynamical rescaling: all of the relaxation times increase identically with the age of the sample. To investigate the microscopic origins of this behaviour, a new numerical analysis technique is developed to identify structural relaxations on the single particle level. The full distribution of relaxation times and displacements is obtained and used to parametrize a continuous time random walk, which reproduces all features of the dynamics, including dynamical rescaling. These results demonstrate that aging is primarily a kinetic phenomenon, due to the wide distribution of relaxation times. So far, neither the average nor the local structural order can explain the aging dynamics.Variations in temperature and deformation can modify the aging dynamics, causing both rejuvenation and overaging (an apparent increase/decrease in the dynamics compared to simple aging). Non-linear creep is shown to accelerate the dynamics and cause an apparent reversal of aging, whereas a temperature step has complex effects on the relaxation times that are impossible to describe as simple rejuvenation or overaging. The effects of parameters such as the temperature, stress, strain, strain rate, and quench history on the apparent age of the sample are investigated through stochastic simulation of the soft glassy rheology model. In this model, rejuvenation due to load predominates, and overaging is observed only under specific conditions of low temperatures, small strains, and high initial energies. Comparison with molecular dynamics simulations shows qualitative agreement, but also identifies several limitations to the model. Investigating the single particle relaxation dynamics under deformation and at different temperatures may enable further improvements of models of plasticity in amorphous solids.
Physical aging in polymer glasses is a nonequilibrium phenomenon characterized byspontaneous processes that lead to changes in almost all physical properties. Whileall glasses undergo physical aging, polymer glasses are among the most widely usedglasses in research and engineering due to their good glass-forming properties andwide applications. This master’s thesis uses molecular dynamics (MD) simulationsto explore recently observed experimental phenomena related to physical aging inpolymer glasses and polymer nanocomposites. Two manuscripts (published and tobe published) have been produced in the duration of this work and are included inchapters 2 and 3.The first manuscript focuses on the effect of mechanical stresses on physical agingin polymer glasses. This is a complicated and controversial subject as experimentalobservations have provided evidence both for and against mechanical rejuvenationand overaging. Specifically, we use MD simulations on a coarse-grained bead springmodel to investigate the stress-enhanced yielding of polymer glasses. Understandingthe origin of this behavior will not only verify whether this can be considered as anexample of mechanically induced overaging; it will facilitate the development of morerealistic constitutive relations for the yield response of glassy polymers, a subject thathas been awarded considerable attention in the last few decades.The second manuscript is concerned with a relatively new area of research, whichinvolves altering the aging behavior of polymer glasses with the addition of nanoscopicfillers. These polymer nanocomposite systems are difficult to explore due to thecomplicated interactions between the fillers and the polymer matrix. Unfortunately,limited experimental work (and no simulation work known to the author) have beendevoted to investigating the physical aging properties of these systems. In this work,we attempt to develop a coarse-grained polymer nanocomposite MD model to studythe impact of nanoparticles on the physical aging behavior of glassy polymers.This thesis should motivate the use of simulations in conjunction with experimentswhen studying physical aging in glasses.