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

Agile software development challenges the traditional way of software development and project management. In rapidly changing environments, changing requirements and tight schedule constraints require software developers to take a different approach toward the process of software development. However, beyond a few case studies, surveys and studies focused on specific practices such as pair programming, the effectiveness and applicability of agile methods have not been established adequately. The objective of my research is to improve the understanding of and gain insights into these issues. For this purpose, I develop a system dynamic simulation model that considers the complex interdependencies among the variety of practices used in agile development. The model is developed on the basis of an extensive review of the literature as well as quantitative and qualitative data collected from real projects in seven organizations. The development of the model was guided by dynamic hypotheses on customer involvement, refactoring and quality of design. The model was refined and validated using data from independent projects. The model helps in answering important questions on the impact of customer behavior, cost of making changes and economics of pair programming. Experimentation with the model suggests that the cost of change is not constant; instead, its value changes cyclically and increases towards the later phase of development. Also, the results of simulation show that with no pair programming, fewer tasks are delivered and it costs more to deliver a task when compared to development with pair programming. Further, customer behavior has a major impact on project performance. The quality of customer feedback is found to be very critical to the successful of an agile software development project. The primary contribution of this research is the simulation model of agile software development that can be used a tool to examine the impact of agile practices and management policies on critical project variables including project scope, schedule, and cost. This research provides a mechanism to study agile development as a dynamic system of practices rather than using a static view and in isolation. The results from this study are expected to be of significant interest to practitioners of agile methods by providing them a simulation environment to examine the impact of their practices, procedures and management policies.

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.

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Relationships between structure and dynamics in fluids have a wide variety of applications. Because theories for fluid structure are now well developed, such relationships can be used to “predict” dynamic properties. Also, recasting dynamic properties in terms of structure may provide new insights. In this thesis, we explore whether some of the relationships between structure and dynamics that have proven useful for understanding simple atomic liquids can also be applied to complex fluid systems. In particular, we focus on model fluid systems with particles that interact with attractive forces that are shortranged (relative to the particle diameter), and display properties that are anomalous when compared to those of simple liquids. Examples of fluids with short-range attractive (SRA) interactions include colloidal suspensions and solutions of micelles or proteins. We show via simulations that common assumptions regarding free volume and dynamics do not apply for SRA fluids, and propose a revision to the traditional free volume perspective of dynamics. We also develop a model which can predict the free volume behavior for hard-sphere and SRA fluids. Next, we demonstrate that the dynamic properties of SRA fluids can be related to structural order. In terms of structural order, the properties of SRA fluids can be related to those of another anomalous fluid, liquid water. In both fluids, anomalous dynamics are closely related to anomalous structure, which can be traced to changes in second and higher coordination shells. We also find that a similar relationship between structural order and dynamics approximately holds for fluids under shear. Motivated by previous work, we explore via simulation how tuning the particle-wall interactions to flatten or enhance the particle layering in a confined fluid impacts its self-diffusivity, viscosity, and entropy. We find that the excess entropy explains the observed trends. Finally, we present preliminary simulation data regarding the relationship between heterogeneous dynamics and structure. We show that the mobility of particles is related in a simple way to the structure of the particles surrounding them. In particular, our results suggest that a critical amount of local disorder allows a particle to be mobile on intermediate time scales. / text

The high demands of manual wheelchair propulsion put users at risk of additional pain and injury that can lead to further reductions in independence and quality of life. Seat position is an adjustable parameter that has been shown to influence propulsion biomechanics. As a result, a number of studies have attempted to optimize this position. However, due to complexities in quantifying upper extremity demand, seat position guidelines are often based on studies aimed at reducing indirect quantities (e.g., cadence, handrim forces, joint ranges of motion and muscle excitation levels) rather than more direct measures of demand (e.g., muscle stress and metabolic cost). Forward dynamics simulations provide an alternative approach to systematically investigate the influence of seat position on more direct measures of upper extremity demand. The objective of this study was to generate and analyze a set of forward dynamics simulations of wheelchair propulsion across the range of attainable seat positions to identify the optimal seat position that minimizes upper extremity demand (i.e., muscle stress, metabolic cost and muscle antagonism). The optimization results showed both metabolic cost and muscle stresses were near minimal values at superior/inferior positions corresponding to top dead center elbow angles between 110 and 120 degrees while at an anterior/posterior position with a hub-shoulder angle between 10 and 2.5 degrees. These minimal values coincided with a reduction in the level of antagonistic muscle activity, primarily at the glenohumeral joint. Seat positions that deviated from these minimal values increased the level of co-contraction required to maintain a stable, smooth propulsive stroke, and consequentially increased upper extremity demand. These results can provide guidelines for positioning the seat to help reduce upper extremity overuse injuries and pain, and thus improve the overall quality of life for wheelchair users. / text

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Polymer nanocomposites (PNCs) have found their way into our everyday lives in a long list of applications, including airplane parts and car tires. This is due to their unique properties of combining the strengths of their constituents – elasticity and stiffness – while mitigating their weaknesses – softness and brittleness. In the past few decades, they have generated more interest due to the discovery that the PNCs’ optical, electrical, and a host of other properties can be tuned for specific use by controlling the assembly and dispersion of nanoparticles (NPs) within the host polymer matrix. The grafting of some of the matrix chains onto the surface of the NPs not only improves NP miscibility but also grants an additional handle tocontrol the self-assembly of NPs. However, at present, there remains many open questions in the field of these novel PNCs. For instance, it is commonly believed that long enough matrix polymers of length P will spontaneously dewet a chemically identical polymer layer, comprised of sufficient chains of length N , end-grafted to a flat surface (”brush”). This entropically driven idea is frequently used to explain experiments in which 10-20 nm diameter polymer-grafted NPs are observed to phase separate from homopolymer matrices for P/N⪆4. At lower grafting densities, these entropic effects are also thought to underpin the self-assembly of grafted NPs into a diverse set of structures. To explore the validity of this picture, a two-pronged approach is used in this thesis, exploring such systems from both a single NP and a multi-NP point of view in order to find novel methods for understanding and controlling NP dispersion in polymers. In each of the chapters, we employ coarse-grained Molecular Dynamics (MD) simulations to understand the self-assembly and dispersion behavior in PNCs, with the experimental analog being primarily polystyrene (PS) grafted silica NPs in PS matrices. We start by investigating the entropic effects of P/N on the brush of a single grafted NP, taking advantage of an indirect umbrella sampling method (INDUS) to quantify matrix density fluctuations. This method essentially makes use of an external biasing potential to mimic the dewetting of the brush. We find for the first time that entropic P/N effects can be identified at the single NP level and is primarily surface driven. INDUS is later extended to two-body and many-body NP systems, to understand the role of NP surfactantcy in the self-assembly of grafted NPs and create free-energy profiles for a range of inter-NP separations. Finally, results from a comprehensive series of large-scale multi-NP simulations, where we consider NPs in the ≈ 5nm and ≈ 10nm size range. For the smaller NPs, we find no evidence of phase separation even for P/N = 10 in the absence of attractions. Instead, we discover that we are able to recreate most of the experimentally observed structures when allthe polymer chain monomers are equally attractive to each other but repel the NPs. Only when the NPs are in the ≈ 10nm size range that we are able to access the phase separated morphologies. Our results thus imply that experimental situations where the grafting density is low are dominated by the surfactancy of the NPs, which is driven by the chemical mismatch between the inorganic core and the organic ligands (the graft and free chains are chemically identical). Entropic effects, i.e. the translational entropy of the NPs and the matrix, the entropy of mixing of the grafts and the matrix, and the conformational entropy of the chains appear to thus play a second order effect even in the context of these model systems. Each of these insights provides details around controlling the organization and assembly of NPs in polymers for the purpose of improving their mechanical properties, all while changing the way in which the material is designed.