Clusters e nanoclusters têm recebido grande atenção devido à suas propriedades físicas e químicas, as quais divergem bastante dos materiais na fase bulk. Essas propriedades podem variar de acordo com a composição e tamanho do cluster. Uma compreensão da evolução das propriedades em relação a estes parâmetros é de grande importância para potencializar diversas aplicações, entretanto, esse entendimento permanece insatisfatório. Este trabalho foi dividido em duas etapas, em que a primeira busca investigar parâmetros energéticos, por meio do cálculo da energia de excesso, e estruturais, analisando parâmetro de ordem química, função de distribuição radial central, comprimento médio de ligação e número de coordenação efetiva, dos sistemas ZrnCum-n, ZrnAlm-n, CunAlm-n e ZrnCunAlm-2n para n = 55 e 561 átomos com o incremento n tomado de 1 em 1 para o sistema de 55 átomos e de 20 em 20 para os sistemas de 561 átomos. A segunda etapa consiste de investigar como variam as propriedades energéticas e estruturais do sistema ZrCu em função da evolução do tamanho do sistema. Para alcançar os objetivos propostos, neste trabalho foi usado o algoritmo de otimização global de clusters e nanopartículas basin-hopping Monte Carlo revisado. O potencial de interação atômica utilizado é o método do átomo imerso, que é bastante utilizado na descrição de sistemas metálicos. Os resultados obtidos sugerem que: (i) os sistemas puros apresentaram energia de coesão mais alta que seu análogo material na fase bulk, sugerindo que estes tendem a aglomerar-se formando estruturas bulk. Para os sistemas binários e ternários, foi identificado que todas as composições são energeticamente estáveis devido aos valores negativos obtidos pelo excesso de energia e, para o sistema ZrCu verificou-se a presença de efeitos de tamanho. (ii) Com relação à estrutura, as composições puras estudadas apresentaram simetria icosaédrica. Para o estudo da evolução do tamanho do sistema, Zr e Cu apresentaram estrutura com simetria icosaédrica até a composição de 561 átomos, além deste tamanho a simetria icosaédrica é quebrada. Para os sistemas binários e ternários foi obtido que os átomos tendem a distribuir-se dentro do nanocluster além de apresentarem quebra da simetria icosaédrica apresentando ausência de camadas atômicas ordenadas acompanhada de redução da coordenação efetiva. Os sistemas ZrCu e ZrAl demonstraram seguir a lei de Vegard, enquanto que os sistemas CuAl e ZrCuAl apresentaram desvio da lei de Vegard providos por efeitos eletrônicos, além de apresentarem a presença de efeitos de tamanho. / Clusters and nanocluster have attracted great attention due to their physical and chemical properties, very different from their analogous bulk. These properties can vary with composition and size cluster. An understanding of the properties evolution with respect these parameters is essential to improve several applications. However, this understanding is not complete. This study was piecemeal in two stage, being the first the investigation of energetic properties, by excess energy analisys, and structural properties, by chemical order parameter, radial distribution function, effective coordination number and average bond length, from ZrnCum-n, ZrnAlm-n, CunAlm-n and ZrnCunAlm-2n systems, where n = 55, 561 atoms and the increment n vary in one unit for 55-atoms system and twenty unit for 561-atoms system. The second stage is the investigation of how vary the energetic and structural properties from the size evolution ZrCu system. To do this study, was employed the global optimization algorith for cluster and nanoparticle Revised basin-hopping Monte Carlo, were this method use the classical calculation to determine the total energy of the system. The interatomic potential used was the embedded atom method, that was very usefull to describe metallic systems. Our results suggest: (i) the unary systems present cohesive energy higher than their analogous bulk, that indicate the trend of clusters to form bulk. To the binary and ternary systems, we had that all systems are favorable to form nanoalloys by negative value of excess energy. From ZrCu system, the stability decrease when increase the size of system. With respect the structure, the unary compounds present icosahedral symmetry. From the size-evolution study, the unary compounds present icosahedral symmetry until 561-atoms composition, after this size the icosahedral symmetry is broken. To binary and ternary systems, the atoms trend form mixture into the nanocluster, the icosahedral symmetry is broken with respect the unary compounds and presenting absence of ordered layers followed by effective coordination reduction. The ZrCu and ZrAl systems follow the Vegard law, while the CuAl and ZrCuAl systems present deviation from Vegard law, because electronic effects.

In this study, we employ molecular statics to construct the structure of amorphous zinc oxide. First, we find out the first number of higher energy structures in all local stable structures by Basin-Hopping algorithm, which are separated into different ratio of crystalline/amorphous zinc oxide structures, and then we judge the type of zinc oxide structure by radial distribution function. In addition, we use coordination number to analyse the interatomic bond length and bond angle in the structures. Furthermore, we employ molecular dynamics to increase the temperature of amorphous zinc oxide structures, and then use the distribution of coordination number, bond length and bond angle between zinc and oxygen atom to analyse the change of the local structure of amorphous zinc oxide during the heating process.

Clusters e nanoclusters têm recebido grande atenção devido à suas propriedades físicas e químicas, as quais divergem bastante dos materiais na fase bulk. Essas propriedades podem variar de acordo com a composição e tamanho do cluster. Uma compreensão da evolução das propriedades em relação a estes parâmetros é de grande importância para potencializar diversas aplicações, entretanto, esse entendimento permanece insatisfatório. Este trabalho foi dividido em duas etapas, em que a primeira busca investigar parâmetros energéticos, por meio do cálculo da energia de excesso, e estruturais, analisando parâmetro de ordem química, função de distribuição radial central, comprimento médio de ligação e número de coordenação efetiva, dos sistemas ZrnCum-n, ZrnAlm-n, CunAlm-n e ZrnCunAlm-2n para n = 55 e 561 átomos com o incremento n tomado de 1 em 1 para o sistema de 55 átomos e de 20 em 20 para os sistemas de 561 átomos. A segunda etapa consiste de investigar como variam as propriedades energéticas e estruturais do sistema ZrCu em função da evolução do tamanho do sistema. Para alcançar os objetivos propostos, neste trabalho foi usado o algoritmo de otimização global de clusters e nanopartículas basin-hopping Monte Carlo revisado. O potencial de interação atômica utilizado é o método do átomo imerso, que é bastante utilizado na descrição de sistemas metálicos. Os resultados obtidos sugerem que: (i) os sistemas puros apresentaram energia de coesão mais alta que seu análogo material na fase bulk, sugerindo que estes tendem a aglomerar-se formando estruturas bulk. Para os sistemas binários e ternários, foi identificado que todas as composições são energeticamente estáveis devido aos valores negativos obtidos pelo excesso de energia e, para o sistema ZrCu verificou-se a presença de efeitos de tamanho. (ii) Com relação à estrutura, as composições puras estudadas apresentaram simetria icosaédrica. Para o estudo da evolução do tamanho do sistema, Zr e Cu apresentaram estrutura com simetria icosaédrica até a composição de 561 átomos, além deste tamanho a simetria icosaédrica é quebrada. Para os sistemas binários e ternários foi obtido que os átomos tendem a distribuir-se dentro do nanocluster além de apresentarem quebra da simetria icosaédrica apresentando ausência de camadas atômicas ordenadas acompanhada de redução da coordenação efetiva. Os sistemas ZrCu e ZrAl demonstraram seguir a lei de Vegard, enquanto que os sistemas CuAl e ZrCuAl apresentaram desvio da lei de Vegard providos por efeitos eletrônicos, além de apresentarem a presença de efeitos de tamanho. / Clusters and nanocluster have attracted great attention due to their physical and chemical properties, very different from their analogous bulk. These properties can vary with composition and size cluster. An understanding of the properties evolution with respect these parameters is essential to improve several applications. However, this understanding is not complete. This study was piecemeal in two stage, being the first the investigation of energetic properties, by excess energy analisys, and structural properties, by chemical order parameter, radial distribution function, effective coordination number and average bond length, from ZrnCum-n, ZrnAlm-n, CunAlm-n and ZrnCunAlm-2n systems, where n = 55, 561 atoms and the increment n vary in one unit for 55-atoms system and twenty unit for 561-atoms system. The second stage is the investigation of how vary the energetic and structural properties from the size evolution ZrCu system. To do this study, was employed the global optimization algorith for cluster and nanoparticle Revised basin-hopping Monte Carlo, were this method use the classical calculation to determine the total energy of the system. The interatomic potential used was the embedded atom method, that was very usefull to describe metallic systems. Our results suggest: (i) the unary systems present cohesive energy higher than their analogous bulk, that indicate the trend of clusters to form bulk. To the binary and ternary systems, we had that all systems are favorable to form nanoalloys by negative value of excess energy. From ZrCu system, the stability decrease when increase the size of system. With respect the structure, the unary compounds present icosahedral symmetry. From the size-evolution study, the unary compounds present icosahedral symmetry until 561-atoms composition, after this size the icosahedral symmetry is broken. To binary and ternary systems, the atoms trend form mixture into the nanocluster, the icosahedral symmetry is broken with respect the unary compounds and presenting absence of ordered layers followed by effective coordination reduction. The ZrCu and ZrAl systems follow the Vegard law, while the CuAl and ZrCuAl systems present deviation from Vegard law, because electronic effects.

Two global optimization methods are proposed in this thesis. They are the multicanonical basin hopping (MUBH) method and the basin paving (BP) method. <br /><br /> The MUBH method combines the basin hopping (BH) method, which can be used to efficiently map out an energy landscape associated with local minima, with the multicanonical Monte Carlo (MUCA) method, which encourages the system to move out of energy traps during the computation. It is found to be more efficient than the original BH method when applied to the Lennard-Jones systems containing 150-185 particles. <br /><br /> The asynchronous multicanonical basin hopping (AMUBH) method, a parallelization of the MUBH method, is also implemented using the message passing interface (MPI) to take advantage of the full usage of multiprocessors in either a homogeneous or a heterogeneous computational environment. AMUBH, MUBH and BH are used together to find the global minimum structures for Co nanoclusters with system size <em>N</em>&le;200. <br /><br /> The BP method is based on the BH method and the idea of the energy landscape paving (ELP) strategy. In comparison with the acceptance scheme of the ELP method, moving towards the low energy region is enhanced and no low energy configuration may be missed during the simulation. The applications to both the pentapeptide Met-enkephalin and the villin subdomain HP-36 locate new configurations having energies lower than those determined previously. <br /><br /> The MUBH, BP and BH methods are further employed to search for the global minimum structures of several proteins/peptides using the ECEPP/2 and ECEPP/3 force fields. These two force fields may produce global minima with different structures. The present study indicates that the global minimum determination from ECEPP/3 prefers helical structures. Also discussed in this thesis is the effect of the environment on the formation of beta hairpins.

Achieving optimal efficiency of production in the industrial sector is a process that is continuously under development. In several industrial installations separators, produced by Alfa Laval, may be found, and therefore it is of interest to make these separators operate more efficiently. The separator that is investigated separates impurities and water from crude oil. The separation performance is partially affected by the settings of process parameters. In this thesis it is investigated whether optimal or near optimal process parametersettings, which minimize the water content in the output, can be obtained.Furthermore, it is also investigated if these settings of a session can be testedto conclude about their suitability for the separator. The data that is usedin this investigation originates from sensors of a factory-installed separator.It consists of five variables which are related to the water content in theoutput. Two additional variables, related to time, are created to enforce thisrelationship. Using this data, optimal or near optimal process parameter settings may be found with an optimization technique. For this procedure, a Gaussian Process with the Deep Kernel Learning extension (GP-DKL) is used to model the relationship between the water content and the sensor data. Three models with different kernel functions are evaluated and the GP-DKL with a Spectral Mixture kernel is demonstrated to be the most suitable option. This combination is used as the objective function in a Basin-hopping optimizer, resulting in settings which correspond to a lower water content.Thus, it is concluded that optimal or near optimal settings can be obtained. Furthermore, the process parameter settings of a session can be tested by utilizing the Bayesian properties of the GP-DKL model. However, due to large posterior variance of the model, it can not be determined if the process parameter settings are suitable for the separator.

Two global optimization methods are proposed in this thesis. They are the multicanonical basin hopping (MUBH) method and the basin paving (BP) method. <br /><br /> The MUBH method combines the basin hopping (BH) method, which can be used to efficiently map out an energy landscape associated with local minima, with the multicanonical Monte Carlo (MUCA) method, which encourages the system to move out of energy traps during the computation. It is found to be more efficient than the original BH method when applied to the Lennard-Jones systems containing 150-185 particles. <br /><br /> The asynchronous multicanonical basin hopping (AMUBH) method, a parallelization of the MUBH method, is also implemented using the message passing interface (MPI) to take advantage of the full usage of multiprocessors in either a homogeneous or a heterogeneous computational environment. AMUBH, MUBH and BH are used together to find the global minimum structures for Co nanoclusters with system size <em>N</em>&le;200. <br /><br /> The BP method is based on the BH method and the idea of the energy landscape paving (ELP) strategy. In comparison with the acceptance scheme of the ELP method, moving towards the low energy region is enhanced and no low energy configuration may be missed during the simulation. The applications to both the pentapeptide Met-enkephalin and the villin subdomain HP-36 locate new configurations having energies lower than those determined previously. <br /><br /> The MUBH, BP and BH methods are further employed to search for the global minimum structures of several proteins/peptides using the ECEPP/2 and ECEPP/3 force fields. These two force fields may produce global minima with different structures. The present study indicates that the global minimum determination from ECEPP/3 prefers helical structures. Also discussed in this thesis is the effect of the environment on the formation of beta hairpins.

The structural and electronic properties of small tungsten nanoparticles Wn (n=2-16) were investigated by density functional theory (DFT) calculation. For the W10 nanoparticle, ten lowest-energy structures were first obtained by basin-hopping method (BH) and ten by big-bang method (BB) with the tight-binding many-body potential for bulk tungsten material. These fifty structures were further optimized by the DFT calculation in order to find the better parameters of tight-binding potential adquately for W nanoparticles. With these modified parameters of tight-binding potentials, several lowest-energy W nanoparticles of different sizes can be obtained by BH and BB methods and then further refined by DFT calculation. According to the values of binding energy and second-order energy difference, it reveals that the structure W12 has a relatively higher stability than those of other sizes. The vertical ionization potential (VIP), adiabatic electron affinity (AEA) and HOMO-LUMO Gap are also discussed for W nanoparticles of different sizes.

In this study, we used the molecular statics, molecular dynamics, and density function theory to investigate structural, electronic, and mechanical properties of ultra-thin silica nanowires. There are two parts in this study. In the first part, we used basin-hopping method to get different diameters of silica nanowires, nemed 2MR, 2MR-2O, 3MR-3O, 4MR-4O, 5MR-5O, 4MR-3f, 4MR-4f, and 4MR-5f. The various silica nanowires were optimized by density function theory to obtain the projected density of states, Mulliken charge, and electronic density difference, and we also compared this results to £\-quartz. In the second part, the molecular dynamics simulations were performed to investigate deformation behavior of silica nanowires under axial tensile loading at 10K. The Young¡¦s modulus increases when the diameter decreases. We also used angular correlation function to study the mechanical properties and variation of structures.

The process of protein and RNA folding has been understood in general terms through the principle of minimal frustration, and is usually thought of as being guided by a folding funnel on the energy landscape, which is based around the native structure. However, more recently, various biomolecules have been associated with multifunnel energy landscapes, where each funnel exhibits a distinct structural ensemble and function. This work explores how the principle of minimal frustration may be extended to multifunnel energy landscapes that are associated with multifunctional biomolecules. To achieve this aim, the computational potential energy landscape framework is employed to analyse four example systems. Additionally, this study analyses mutants for all four systems, where the mutations are chosen to change properties of the systems without destabilising the native sequence ensemble entirely. The first system considered is a two-state coiled-coil. It is shown how mutations fundamentally change the energy landscape from the minimal frustrated organisation necessary to fulfil biological function. These changes can introduce alternative pathways for folding, as well as new structural ensembles. Similar effects are observed for ubiquitin. In addition, the landscape exploration allows us to calculate a number of experimentally determined properties for this protein, which exhibit excellent agreement, and we characterise folding at an atomistic level of detail. Next we consider the hormones oxytocin and vasopressin, which are themselves mutants of each other, along with a number of other mutants for both molecules. Again, the frustration in the landscape increases due to mutations, and a greater variety in the resulting structural ensembles is observed, leading to changes in binding affinities. Finally, the HP1 loop of RNA 7SK is analysed, revealing that the principles established for the energy landscapes of proteins extend to nucleic acids. Overall, the results indicate that sequences have evolved to exhibit the minimum number of funnels on the energy landscape to support multiple functions, extending the principle of minimal frustration to multifunnel energy landscapes.

In this project, various computational energy landscape methods were accelerated using graphics processing units (GPUs). Basin-hopping global optimisation was treated using a version of the limited-memory BFGS algorithm adapted for CUDA, in combination with GPU-acceleration of the potential calculation. The Lennard-Jones potential was implemented using CUDA, and an interface to the GPU-accelerated AMBER potential was constructed. These results were then extended to form the basis of a GPU-accelerated version of hybrid eigenvector-following. The doubly-nudged elastic band method was also accelerated using an interface to the potential calculation on GPU. Additionally, a local rigid body framework was adapted for GPU hardware. Tests were performed for eight biomolecules represented using the AMBER potential, ranging in size from 81 to 22\,811 atoms, and the effects of minimiser history size and local rigidification on the overall efficiency were analysed. Improvements relative to CPU performance of up to two orders of magnitude were obtained for the largest systems. These methods have been successfully applied to both biological systems and atomic clusters. An existing interface between a code for free energy basin-hopping and the SuiteSparse package for sparse Cholesky factorisation was refined, validated and tested. Tests were performed for both Lennard-Jones clusters and selected biomolecules represented using the AMBER potential. Significant acceleration of the vibrational frequency calculations was achieved, with negligible loss of accuracy, relative to the standard diagonalisation procedure. For the larger systems, exploiting sparsity reduces the computational cost by factors of 10 to 30. The acceleration of these computational energy landscape methods opens up the possibility of investigating much larger and more complex systems than previously accessible. A wide array of new applications are now computationally feasible.