In this thesis, molecular dynamics simulations were performed to characterize the atomic motions governing grain boundary migration in a series of [001] twist boundaries. Particularly, migrations of a =36.87 5, a =22.63 13 and a =40.23 general high angle [001] twist boundaries driven by stored elastic energy in fcc Ni were investigated. Atomic motions during migration were identified as the combination of single atom jump and string-like cooperative atomic motions. The simulation results confirmed that the collective 4-atom shuffle motion was the rate controlling atomic motion during the migration of 5 twist boundary. As grain boundary local symmetry decreasing, string-like cooperative atomic motions became increasingly important. Eventually, both random single atom jump and string-like cooperative motions became dominant during the migration of general non- twist boundary. Furthermore, simulations showed that activation energy for grain boundary migration was well correlated with the average string length occurring within boundary. / Materials Engineering

The main focus of my dissertation is on the conformational motion of DNA, studied by applying tools from the computational chemistry field. In addition, studies of relative α- and 310 helical stabilities in peptides/mini-proteins, and a molecular flooding study of the retinoid X-receptor as part of a continuing drug design effort are presented. In molecular biology, it has been well known that sequence determines structure, and structure controls function. For proteins or DNA to work properly, the correct configuration is required. Mutations may alter the structure, which can cause malfunction. Non-mutational effects, such as a change in environment may also cause a configurational change and in turn change the functionality of the protein or DNA. Many experimental technics have been developed to investigate the structural or configurational aspects of biological systems, and molecular dynamics simulation has been proven to be a useful complementary tool to gain insights into this problem due to its ability to explore the dynamics and energetics of biomolecular processes at high spatial and time resolution. Molecular dynamics simulations are constrained by the available computational power, but several computational techniques have been developed to reduce computational costs. Also, development of hardware has helped the issue. Years of hard work on force field parameter optimization built a solid foundation for molecular dynamics simulations, so that the computational model can satisfactory describe many biochemical systems in detail. Techniques such as umbrella ix sampling and reweighting methods have allowed researchers to construct free energy landscapes to reveal the relative stabilities of each major configurational state and the free energy barriers between configurations from relatively short simulations, a process which would otherwise require many microseconds of unbiased simulations. My dissertation applies multiple advanced simulation techniques to investigate several DNA conformational problems, including the coupling between DNA bending and base flipping, the anisotropy of DNA bending, and intercalation of the dye in a Cy3 labeled DNA system. The main part of this work addressed a long standing question about DNA bending: does DNA prefer to bend toward the major or minor groove. My simulations not only answered this question, but also identified the mechanism by which the one direction is favored. Another part describes peptide/mini-protein helical transitions and studies benefiting ligand design for the retinoid X-receptor.

Indiana University-Purdue University Indianapolis (IUPUI) / Atomistic simulations are used in this project to study the deformation mechanism of polycrystalline and bicrystal of pure Al and Al-Mg alloys. Voronoi Tessellation was used to create three-dimensional polycrystalline models. Monte Carlo and Molecular Dynamics simulations were used to achieve both mechanical and chemical equilibrium in all models. The first part of the results showed improved strength, which is included the yield strength and ultimate strength in the applied tensile loading through the addition of 5 at% Mg to nanocrystalline aluminum. By viewing atomic structures, it clearly shows the multiple strengthening mechanisms related to doping in Al-Mg alloys. The strength mechanism of dopants exhibits as dopant pinning grain boundary (GB) migration at the early deformation stage. At the late stage where it is close to the failure of nanocrystalline materials, Mg dopants can stop the initiation of intergranular cracks and also do not let propagation of existing cracks along the GBs. Therefore, the flow stress will improve in Al-Mg alloy compared to pure Al. In the second part of our results, in different bicrystal Al model, ∑ 3 model has higher strength than other models. This result indicates that GB structure can affect the strength of the material. When the Mg dopants were added to the Al material, the strength of ∑5 bicrystal models was improved in the applied shear loading. However, it did not happen for ∑ 3 model, which shows Mg dopants cannot affect the behavior of this GB significantly. Analysis of GB movements shows that Mg dopants stopped GBs from moving in the ∑ 5 models. However, in the ∑ 3 GB, displacement of grain boundary planes was not affected by Mg dopants. Therefore, the strength and flow stress are improved by Mg dopants in ∑ 5 Al GBs, not in the ∑ 3 GBs.

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<div>Atomistic simulations are used in this project to study the deformation mechanism of polycrystalline and bicrystal of pure Al and Al-Mg alloys. Voronoi Tessellation was used to create three-dimensional polycrystalline models. Monte Carlo and Molecular</div><div>Dynamics simulations were used to achieve both mechanical and chemical equilibrium in all models. The first part of the results showed improved strength, which is included the yield strength and ultimate strength in the applied tensile loading through the addition of 5 at% Mg to nanocrystalline aluminum. By viewing atomic structures, it clearly shows the multiple strengthening mechanisms related to doping in Al-Mg alloys. The strength mechanism of dopants exhibits as dopant pinning grain boundary (GB) migration at the early deformation stage. At the late stage where it is close to the failure of nanocrystalline materials, Mg dopants can stop the initiation of intergranular cracks and also do not let propagation of existing cracks along the GBs. Therefore, the flow stress will improve in Al-Mg alloy compared to pure Al. In the second part of our results, in different bicrystal Al model, Σ 3 model has higher strength than other models. This result indicates that GB structure can affect the strength of the material. When the Mg dopants were added to the Al material, the strength of sigma 5 bicrystal models was improved in the applied shear loading. </div><div><br></div><div>However, it did not happen for Σ 3 model, which shows Mg dopants cannot affect the behavior of this GB significantly. Analysis of GB movements shows that Mg dopants stopped GBs from moving in the Σ 5 models. However, in sigma 3 GBs, displacement of grain boundary planes was not affected by Mg dopants. Therefore, the strength and flow stress are improved by Mg dopants in Σ 5 Al GBs, not in the Σ 3 GB.</div>

The fundamental structure of all biological membranes is the lipid bilayer. At- tributed to the multifaceted features of lipids and its dynamical interaction with other membrane-integrated molecules, the lipid bilayer is involved in a variety of physiological phenomena such as transmembrane transportation, cellular signalling transduction, energy storage, etc. Due to the nanoscale but high complexity of the lipid bilayer system, experimental investigation into many important processes at the molecular level is still challenging. Molecular dynamics (MD) simulation has been emerging as a powerful tool to study the lipid membrane at the nanoscale. Utilizing atomistic MD, we have quantitatively investigated the effect of lamellar and nonlamellar lipid composition changes on a series of important bilayer properties, and how membranes behave when exposed to a high-pressure environment. A series of membrane properties such as lateral pressure and dipole potential pro les are quanti ed. Results suggest the hypothesis that compositional changes, involving both lipid heads and tails, modulate crucial mechanical and electrical features of the lipid bilayer, so that a range of biological phenomena, such as the permeation through the membrane and conformational equilibria of membrane proteins, may be regulated. Furthermore, water also plays an essential role in the biomembrane system. To balance accuracy and efficiency in simulations, a coarse-grained ELBA water model was developed. Here, the ELBA water model is stress tested in terms of temperature- and pressure-related properties, as well as hydrating properties. Results show that the accuracy of the ELBA model is almost as good as conventional atomistic water models, while the computational efficiency is increased substantially.

In recent years, the use of self-associating block copolymer based drug delivery systems have attracted increasing attention as nanoscopic carriers for the encapsulation and the controlled delivery of water insoluble drugs. Currently, most of the drug formulations proceed by trial and error method with no distinct method to predict the right combination of block copolymers and drugs to give all the desired functional properties. This is simply because such drug delivery systems involve complex intermolecular interactions and geometric fitting of molecules of different shapes. So, in the context of block copolymer design process, quantification and prediction of the interactions between potential block copolymers and the target drug are of great importance. Computer simulations that can predict the level and type of interactions encountered in drug/block copolymer pairs will enable researchers to make educated decisions on choosing a particular polymeric carrier for a given drug, avoiding time consuming and expensive trial and error based formulation experiments. In the present thesis, we reported the use of molecular dynamics (MD) simulation to predict the solubility of sets of hydrophobic drug molecules having different spatial distribution of hydrogen bond forming moieties in a series of micelle-forming PEO-b-PCL block copolymers with and without functionalized PCL blocks. The solubility predictions based on the MD results were then compared with those obtained from the solubility experiments and those obtained by the commonly used group contribution method (GCM). MD analysis techniques like radial distribution functions provided useful atomistic details to understand the molecular origin of miscibility and/or immiscibility observed between drugs and di-block copolymers. Based on the evidence of reported work, intermolecular specific interactions, intra-molecular interactions, local molecular packing, and stereochemistry of the hydrophobic block all play important roles in inducing miscibility between drugs and block copolymers. Additionally, not only the architecture of block copolymers but also the molecular characteristics of drug molecules, e.g., spatial distributions of hydrogen bond donors and acceptors on their molecules can affect the miscibility characteristics of binary mixtures. Depending on the groups present on drugs and block copolymers, any of the above factors can play vital role in the process of favouring encapsulation. The understanding of relative contributions of these interactions can help us to customize the performance of drug carriers by engineering the structure of block copolymers. / Chemical Engineering

The present thesis honors contemporary molecular dynamics simulation methodologies which provide powerful means to predict data, interpret observations and widen our understanding of the dynamics, structures and interactions of carbohydrate systems. With this as starting point my thesis work embarked on several cutting edge problems summarized as follows. In my first work the thermal response in crystal cellulose Iβ was studied with special emphasis on the temperature dependence of the crystal unit cell parameters and the organization of the hydrogen bonding network. The favorable comparison with available experimental data, like the phase transition temperature, the X-ray diffraction crystal structures of cellulose Iβ at room and high temperatures, and temperature dependent IR spectra supported our conclusions on the good performance of the GLYCAM06 force field for the description of cellulose crystals, and that a cautious parameterization of the non-bonded interaction terms in a force field is critical for the correct prediction of the thermal response in cellulose crystals. The adsorption properties of xyloglucans on the cellulose Iβ surface were investigated in my second paper. In our simulations, the interaction energies between xyloglucan and cellulose in water were found to be considerably lower than those in vacuo. The van der Waals interactions played a prevailing role over the electrostatic interactions in the adsorption. Though the variation in one side chain did not have much influence on the interaction energy and the binding affinity, it did affect the structural properties of the adsorbed xyloglucans. The interaction of the tetradecasaccharide XXXGXXXG in complex with the hybrid aspen xyloglucan endo-transglycosylase PttXET16-34 was studied in the third paper. The effect of the charge state of the “nucleophile helper” residue Asp87 on the PttXET16-34 active site structure was emphasized. The results indicate that the catalysis is optimal when the catalytic nucleophile is deprotonated, while the “helper” residue and general acid/base residue are both protonated. In my forth paper, the working mechanism for a redox-responsive bistable [2]rotaxane based on an α-cyclodextrin ring was investigated. The umbrella sampling technique was employed to calculate the free energy profiles for the shuttling motion of the α-cyclodextrin ring between two recognition sites on the dumbbell of the rotaxane. The calculated free energy profiles verified the binding preferences observed experimentally. The driving force for the shuttling movement of the α-cyclodextrin ring was revealed by the analysis of the free energy components. / QC 20110513

The Co-Cu nanoparticles is one of the magnetic materials that have considerable potential for a variety of industrial applications, including giant magnetoresistance (GMR) digital storage devices and have therefore attracted a great deal of attention in recent years. For this reason, it will be an important reference to the development of the magnetic digital storage devices if we can go deep into study the material properties of the Co-Cu nanoparticles. This study uses molecular dynamics simulations to investigate the crystalline process of Co-Cu nanoparticles of high and low Co concentrations (5~25 %) during the annealing process. The modified many-body tight binding potential is adopted to accurately model the Cu-Cu, Co-Co, and Co-Cu pair inter-atomic interactions. The structural transformations at the upper and lower melting points are observed by the radial distribution function (RDF), the angle correction function (ACF) and the average bond lengths. finally, we employs molecular dynamics simulations to predict the distribution function of diluted magnetic Co atoms in a Cu host and then uses the the Ruderman-Kittel-Kasuya-Yosida (RKKY) theory and quantum magnetism theory to calculate the magnetic properties of the Co-Cu alloys at different temperature, including their Curie temperature.