Browsing by study line "Computational Materials Physics"
Now showing items 1-12 of 12
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(2022)In this thesis, sputtering of several low- and high-index tungsten surface crystal directions are investigated. The molecular dynamics study is conducted using the primary knock-on atom method, which allows for an equal energy deposition for all surface orientations. The energy is introduced into the system on two different depths, on the surface and on a depth of 1 nm. Additionally to the sputtering yield of each surface orientation, the underlying sputtering process is investigated. Amorphous target materials are often used to compare sputtering yields of polycrystalline materials with simulations. Therefore, an amorphous surface is also investigated to compare it's sputtering yield and process with crystalline surface orientations. When the primary knock-on atom was placed on the surface all surface orientations had a cosine shaped angular distribution with little variation in the sputtering yield for most of the surface orientations. Linear collision sequences were observed to have a large impact on the sputtering yield when the energy was introduced deeper inside the material. In these linear collision sequences the recoils are traveling along the most close packed atom rows in the material. The distance from the origin of the collision cascade to the surface in the direction of the most close packed row is therefore crucial for the sputtering yield of the surface. Surface directions with high angles between this direction and the surface normal hence show a reduction in the sputtering yield. The amorphous material had a little lower sputtering yield than the crystalline materials when the primary knock-on atoms was placed on the surface whereas the difference rose into several orders of magnitude when the energy was given at 1 nm. It is impossible for linear collision sequences to propagate long distances in the amorphous material and therefore the angular distribution in both cases is cosine shaped. The amorphous material has no long range order and was therefore unable to reproduce the linear collision sequences, which are characteristic for the crystalline materials. The difference in the sputtering yield was hence up to several orders of magnitude as a result when the energy was introduced at 1 nm depth.
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(2022)Amorphous metal oxides have proven to deform in a plastic manner at microscopic scale. In this study the plastic deformation and elastic properties of amorphous metal oxides are studied at microscopic scale using classical molecular dynamics simulations. Amorphous solids differ from crystalline solids by not having a regular lattice nor long range order. In this study the amorphous materials were created in simulations by melt-quenching. The glass transition temperature (Tg) depends on the material and cooling rate. The effect of cooling rate was studied with aluminiumoxide (Al2O3) by creating a simulation cell of 115 200 atoms and melt-quenching it with cooling rates of 1011 , 1012 and 1013 K/s. It was observed that faster cooling rates yield higher Tg. The Al2O3 was cooled to 300 K and 50 K after which the material was stretched. The stress-strain curve of the material showed that samples with higher Tg deforms in plastic manner with smaller stresses. The system stretched at 50 K had higher ultimate tensile strength than the system stretched at 300 K and thus confirming the hypothesis proposed by Frankberg about activating plastic flow with work. In order to see if the plastic phenomena can be generalized to other amorphous metal oxides the tensile simulation was performed also with a-Ga2O3 by creating a simulation cell of 105 000 atoms, melt-quenching it and then stretching. Due to the lack of parameters for Buckingham potential these parameters were fitted with GULP using the elastic properties and crystalline structure of Ga2O3. The elastic properties of Ga2O3 with the fitted potential parameters agreed very well with the literature values. The elongated a-Ga2O3 behaved in a very similar fashion compared to a-Al2O3 cooled with the same cooling rate. Further work is needed to establish the Buckingham potential parameters of a-Ga2O3 by experimen tal work. The potential can also be developed further by using the elastic constants and structures of amorphous a-Ga2O3 in the fitting process, although the potential shows already very promising results.
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(2023)The diffusion of a single hydrogen atom through solid tungsten was studied using two separate computational methods: Molecular dynamics simulations and nudged elastic band calculations. Molecular dynamics was used to track the atom’s path in the tungsten lattice in several successive simulations to obtain its mean squared displacement. Results were obtained for temperatures between 400 K and 700 K. These were used to derive a temperature relation for the diffusion coefficient and an estimate for the diffusion energy barrier, which was 0.1985 eV. The nudged elastic band method was used to directly obtain an estimate for the diffusion energy barrier. The same tungsten lattice system as in the molecular dynamics simulations had the hydrogen atom relaxed into an interstitial position and then moved over the energy barrier into an adjacent site. If the tungsten atoms were allowed to relax during the motion, a comparable value of 0.2022 eV was obtained. Further computations were made with a fixed-length tungsten bond next to the hydrogen starting position, yielding energy barriers from 0.1 eV to 1.2 eV depending on the bond length, direction of the diffusion jump and tungsten relaxation. In conclusion, the two different computational methods do give results for the energy barrier that are comparable in magnitude, but further measurement of the tungsten bonds near the hydrogen atom during the molecular dynamics simulation may be needed for a more matching comparison from the nudged elastic band results.
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(2022)The complex physical mechanisms involved in the formation of vacuum arcs have been of interest for many decades. Vacuum arcs are relevant in many engineering disciplines, but the physics behind them is not yet fully understood. In recent years, there have been many experimental and computational studies focused on understanding aspects of vacuum arcs. This thesis focuses on further development of a simulation model to describe the physical processes starting from electron emission and leading to the formation of an ionized plasma. The FEMOCS code is extended to include plasma simulation based on previous work on ArcPIC. Emission of electrons and heating of the cathode is simulated using the finite element method, while plasma simulation is performed using the particle-in-cell method. We add evaporation of neutral atoms from the cathode, as well as ionization processes for multiple species of ions. Monte Carlo collisions for elastic, Coulomb, impact ionization, charge exchange and recombination collisions between particles are added. Direct field ionization of neutrals is included to account for ionization at high electric fields. A dynamic weighting scheme is described for adjusting superparticle weights during the simulation. Ion bombardment effects such as bombardment heating and sputtering are added to account for additional supply of neutrals resulting from energetic ions accelerated by the electric field. Finally, we add a circuit model for coupling to an external circuit. A static nanotip is simulated with different parameters to study local field thresholds leading to thermal runaway. We find that our simulations agree with experimental results. The most significant interactions contributing to initial formation of vacuum arcs are identified. We find most neutrals are created via evaporation rather than sputtering. The most important collision for plasma formation is impact ionization of neutrals into Cu+ ions, while higher-order ions are found to play a lesser role. Direct field ionization of neutrals is also found to be significant at high fields on the order of 10 GV/m.
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(2022)NMDA receptors are ionotropic glutamate receptors (iGluRs), tetrameric proteins, mediating synaptic transmission in the brain and the whole nervous system. Together with another type of iGluRs, AMPA receptors, they are considered essential for neuronal plasticity and memory. Understanding their dynamics and different kinetics is vital for studying various neurological diseases. The relatively slow dynamics, where the time scales of related processes range up to hundreds of milliseconds, make studying them with Molecular Dynamics (MD) simulations challenging. We developed the Functional Sampling Tool (FST), a novel method for enhancing the sampling of a function of interest. Compared to existing enhanced sampling schemes it strikes a balance between generality and simplicity, minimising the need of user input, while allowing for maximal customisability. Using FST, we studied two processes of the NMDA receptor. By keeping all four ligands bound we simulated a desensitisation pathway, and by removing all four we simulated an inactivation pathway. The tool sampled both, giving a good distribution between open and closed states. The tool also allowed us to change the function in the middle of sampling. With the new function we were able to produce more data, focusing on a certain value range.
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(2023)This thesis examines the implementation of general purpose graphics processing unit (GPGPU) acceleration to a non-equilibrium Green’s function (NEGF) equation solver in the context of a computational photoelectrochemical (PEC) cell model. The goal is to find out whether GPGPU acceleration of the NEGF equation solver is a viable option. The current model does not yet have electron-photon scattering, but from the results it is possible to assess the viability of GPGPU acceleration in the case of a complete PEC cell model. The viability of GPGPU acceleration was studied by comparing the performance difference of two graphics processing unit (GPU) solutions against a multi core central processing unit (CPU) solution. The difference between the two GPU solutions was in the used floating-point precision. The GPU solutions would use LU factorization to solve the NEGF equations, and the CPU solution a banded solver (Gauss tridiagonal) provided by Scipy Python package. The performance comparison was done on multiple different GPU and CPU hardware. The electrical transport properties of the PEC cell were modeled by a self-consistent process in which the NEGF and Poisson equations were solved iteratively. The PEC cell was described as a semiconductor device connected with a metal and electrolyte contacts. The device was assumed to be a simple one dimensional tight-binding atom chain made of GaAs, where the transverse modes in the y–z plane are treated with a logarithmic function. The computational model did lack electron-photon scattering, which would be implemented in the future. From the benchmark results, it can be concluded that the GPGPU acceleration via LU factorization is not a viable option in the current code or in the complete model with electron-photon scattering and the assumed approximations. The parallel multi-core CPU code generally outperformed the GPU codes. The key weakness of the GPU code was the usage of LU factorization. Despite of this, there could be an opportunity for GPGPU acceleration if a more complex lattice structure and more exact scattering terms would be used. Also, a GPU accelerated tridiagonal solver could be a possible solution.
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(2023)Quantum Monte Carlo (QMC) is an accurate but computationally expensive technique for simulating the electronic structure of solids, with its use as a simulation technique for modelling positron states and annihilation in solids relatively new. These simulations can support positron annihilation spectroscopy and help with defect characterisation in solids and vacancy identification by calculating the positron lifetime with increased accuracy and comparing them to experimental results. One method of reducing the computational cost of simulations whilst maintaining chemical accuracy is to employ pseudopotentials. Pseudopotentials are a method to approximate the interactions between the outer valence electrons of an atom and the inner core electrons, which are difficult to model. By replacing the core electrons of an atom with an effective potential, a level of accuracy can be maintained whilst reducing the computational cost. This work extends existing research with a new set of pseudopotentials with fewer core electrons replaced by an effective potential, leading to an increase in the number of core electrons in the simulation. With the inclusion of additional core electrons into the simulation, the corrections that need to be made to the positron lifetime may not be needed. Silicon is chosen as the element under study as the high electron count makes it difficult to model accurately for positron simulations. The suitability of these new pseudopotentials for QMC is shown by calculating the cohesive and relaxation energy with comparisons made to previously used pseudopotentials. The positron lifetime is calculated from QMC simulations and compared against experimental and theoretical values. The simulation method and challenges due to the inclusion of more core electrons are presented and discussed. The results show that these pseudopotentials are suitable for use in QMC studies, including positron lifetime studies. With the inclusion of more core electrons into the simulation a positron lifetime was calculated with similar accuracy to previous studies, without the need for corrections, proving the validity of the pseudopotentials for use in positron studies. The validation of these pseudopotentials enables future theoretical studies to better capture the annihilation characteristics in cases where core electrons are important. In achieving these results, it was found that energy minimisation rather than variance minimisation was needed for optimising the wavefunction with these pseudopotentials.
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(2021)This thesis focuses on the initial measurements and development of a 1.5K target temperature cryostat to contain all quantum standards in the quantum metrological triangle. Currently, the cryostat can reach 4.2K end temperature with a cryocooler to liquefy helium for cooling experiments related to the quantum standards of SI-units which require 1.5K end temperature and the 1.5K cooling circuit is one of the research questions of the thesis for future development of the cryostat. Measurements included cooling cycles in a helium environment for liquefaction, as well as no load conditions. Results of the experimentation conclude that liquefaction was unsuccessful at this stage, but could be achieved with improved temperature control. The thesis is based on experimental work carried out in VTT technical research center of Finland, during the course of which the cryostat was progressively developed towards the future utility of combining experiments that realize the quantum standards of Ampere, voltage and resistance under a single low temperature experimental platform, the unified quantum standard cryostat.
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(2023)Ga2O3 has been found to exhibit excellent radiation hardness properties, making it an ideal candidate for use in a variety of applications that involve exposure to ionizing radiation, such as in space exploration, nuclear power generation, and medical imaging. Understanding the behaviour of Ga2O3 under irradiation is therefore crucial for optimizing its performance in these applications and ensuring their safe and efficient operation. There are five commonly identified polymorphs of Ga2O3 , namely, β, α, γ, δ and structures, among these phases, β-Ga2O3 is the most stable crystal structure and has attracted majority of the recent attention. In this thesis, we used molecular dynamic simulations with the newly developed machine learned Gaussian approximation potentials to investigate the radiation damage in β-Ga2O3 . We inspected the gradual structural change in β-Ga2O3 lattice with increase doses of Frenkel pairs implantations. The results revealed that O-Frenkel pairs have a strong tendency to recombine and return to their original sublattice sites. When Ga- and O-Frenkel pairs are implanted to the same cell, the crystal structure was damaged and converted to an amorphous phase at low doses. However, the accumulation of pure Ga-Frenkel pairs in the simulation cells might induce a transition of β to γ-Ga, while O sublattice remains FCC crystal structure, which theoretically demonstrated the recent experiments finding that β- Ga2O3 transfers to the γ phase following ion implantation. To gain a better understanding of the natural behaviour of β-Ga2O3 under irradiation, we utilized collision cascade simulations. The results revealed that O sublattice in the β-Ga2O3 lattice is robust and less susceptible to damage, despite O atoms having higher mobility. The collision and recrystallization process resulted in a greater accumulation of Ga defects than O defects, regardless of PKA atom type. These further revealed that displaced Ga ion hard to recombine to β- Ga lattice, while the FCC stacking of the O sublattice has very strong tendency to recovery. Our theoretical models on the radiation damage of β-Ga2O3 provide insight into the mechanisms underlying defect generation and recovery during experiment ion implantation, which has significant implications for improving Ga2O3 radiation tolerance, as well as optimizing its electronic and optical properties.
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(2022)Energy is an essential input for any non-spontaneous mechanism. In biological organisms, the process of producing energy currency, adenosine triphosphate, is called cellular respiration. It is made of three smaller steps, out of which the last one is oxidative phosphorylation that is responsible for the largest production of adenosine triphosphate molecules in the whole process. Oxidative phosphorylation is performed by the electron transport chain made of five protein complexes, named respiratory complex I-V. Complex I is the first and largest protein complex in the electron transport chain, and it is the least understood. Its primary function is to transfer electrons from nicotinamide adenine dinucleotide to ubiquinone, which is coupled to the pumping of four protons across the mitochondrial inner membrane. Although the overall reaction of complex I is understood, the intricate detail of the mechanism is still largely unknown. There is significance in the details because there are numerous point mutations, which have been strongly correlated with neurogenerative diseases, such as Leigh’s syndrome, and aging. Therefore, a more thorough understanding of its mechanism can give insight into potential target drug development. Complex I is made of 14 highly conserved subunits that can be found in most species that use the electron transport chain. They create an L-shape, where seven subunits are embedded in the inner membrane, the membrane domain, and the others are floating in the mitochondrial matrix, the peripheral arm. In mitochondrial complex I, however, there are in addition around 30 accessory subunits. It has been previously thought that the main mechanism is conducted by the 14 subunits that are found in all species. However, in the past couple of years, it has been shown that accessory subunits can play an important role in the mechanism of mitochondrial complex I. The work presented in this thesis uses a multiscale computational approach to study the effect of three mutations, F89A, Y43A and L42A, from an accessory subunit LYRM6 on the function of complex I. Previous experiments demonstrated that the mutations decreased the overall activity of complex I by 76-86 %. The LYRM6 subunit is located at the pivot of the membrane and periplasmic domains. The results of this study show that the point mutations have a long-range effect on the conformations of three loops from three conserved subunits in this region. The shift in the loop dynamics causes a drop in water occupancy. The observed water pathway is tested for the capability of proton transfer. The findings are demonstrated with the help of molecular dynamics and quantum mechanics/molecular mechanics simulations.
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(2022)The crystal structure of magnetite (Fe3O4) involves Fe2+ ions in sites with octahedral (Oh) symmetry and Fe2+ and Fe3+ ions in sites with tetrahedral (Td) symmetry. Magnetite exhibits several interesting physical phenomena, such as the Verwey transition, in which the roles of the different Fe sites are an active subject of research. In the X-ray standing wave (XSW) technique, incoming and diffracted X-ray beams interfere inside a crystal, creating a standing wave with the periodicity of the diffracting atomic lattice. The phase of the wave, i.e. whether the nodes are located on the lattice planes or between them, can be adjusted by finely tuning the diffraction angle. Changing the phase in this way makes it possible to selectively vary the contributions of different atoms and absorption types (dipole versus quadrupole) to the measured total absorption spectrum. Iron K-edge absorption spectra in magnetite were studied in the presence of an XSW in an experiment conducted at the European Synchrotron Radiation Facility (ESRF) in Grenoble, France. This thesis presents an analysis of the data gathered during the experiment, with the goal of decomposing the experimentally measured pre-edge peak into its constituent components. The methods used in the analysis include principal component analysis and fitting predicted absorption peaks calculated with the Quanty software to the experimental data. The results show the dipole and quadrupole contributions of the tetrahedral sites responding to changes in the phase of the XSW in opposite ways in a manner consistent with theoretical predictions.
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(2023)High-entropy alloys (HEAs), esteemed for their exceptional resistance to radiation damage, carry considerable potential for deployment within fusion reactors. Nonetheless, due to their compositional complexity, comprehending the diffusion behaviour in these multifaceted alloys continues to be a daunting task. This thesis proposes a novel approach to modelling vacancy diffusion in body-centred cubic (BCC) HEAs, particularly Mo-Nb-Ta-V-W. The methodology involves the tactical application of collective variable-driven hyperdynamics (CVHD) to procure data for training a Gaussian process regression (GPR) and feed-forward neural network (FNN) model. The trained FNN model is subsequently employed within kinetic Monte Carlo (KMC) simulations for accurately predicting jump rates, whereas the GPR model is used to elucidate experimental findings related to the behaviour of vacancies in \mbox{Mo-Nb-Ta-V-W}. The robustness of the FNN model is manifested by its capacity to generalise to unseen data, whilst the efficacy of the overall method is corroborated by Monte Carlo molecular dynamics (MCMD) simulations. The CVHD methodology, uniquely capable of functioning at finite temperatures, can capture the entropic contribution to the free energy and model kinematics explicitly. This singular ability facilitates a more comprehensive understanding of the system's behaviour under authentic conditions. The findings presented in this thesis signify a considerable stride forward in the study of HEAs, providing a robust framework for the design of advanced materials. These results underscore the potential of the CVHD-trained FNN-KMC methodology in exploring complex environments, thereby establishing a firm foundation for future investigations and emphasising the need for its continued refinement and augmentation.
Now showing items 1-12 of 12