In this work flow properties of dendrimers are studied with the aid of molecular simulations. For the first time the results of the nonequilibrium molecular dynamics simulations of the dendrimers in the melt are reported. Molecules are modelled at the coarse-grained level using the bead-spring model. The objective of this research is to analyse the influence of the molecular topology in the macroscopic flow behaviour of the melts. Systems of dendrimers of generations 1 to 4 undergoing planar shear are compared to the melts composed of linear chain polymers. The internal structure and shape of dendrimers is extensively analysed. The response of the molecules to the shearing in the form of stretching and alignment is studied. The correlation between the onset of shear thinning and the onset of deformation of molecules is observed. The changes in the fractal dimensionality of dendrimers due to shearing are also analysed. Dendrimers, due to their highly branched structure and compact globular conformations in the melt, are found to behave differently when sheared, compared to traditional linear polymers. Unlike linear polymers, they do not undergo transition form the Rouse to the reptation regimes. This effect is explained in terms of the suppressed entanglement between molecules. Moreover, dendrimers when compared to linear chain systems exhibit lower Newtonian viscosity, onset of the shear thinning at higher strain rates, and less pronounced shear thinning in the non-Newtonian regime. They can be used as rheology modifiers, as it is shown in the preliminary results obtained from the simulations of the dendrimers-linear polymer blends. In agreement with other theoretical and experimental studies, dendrimers in the melt are found to have compact space-filling structure with terminal groups distributed throughout the interior of the molecule. Suggestions for the further study of dendrimers via molecular simulations are made.

The aim of this work is to use molecular simulation to investigate the role of three-body interatomic potentials in noble gas systems for two distinct phenomena: phase equilibria and shear flow. In particular we studied the vapour-liquid coexisting phase for pure systems (argon, krypton and xenon) and for an argon-krypton mixture, utilizing the technique called Monte Carlo Gibbs ensemble. We also studied the dependence of the shear viscosity, pressure and energy with the strain rate in planar Couette flow, using a non-equilibrium molecular simulation (NEMD) technique. The results we present in this work demonstrate that three-body interactions play an important role in the overall interatomic interactions of noble gases. This is demonstrated by the good agreement between our simulation results and the experimental data for both equilibrium and non-equilibrium systems. The good results for vapour-liquid coexisting phases encourage performing further computer simulations with realistic potentials. This may improve the prediction of quantities like critical temperature and density, in particular of substances for which these properties are difficult to obtain from experiment. We have demonstrated that use of accurate two- and three-body potentials for shearing liquid argon and xenon displays significant departure from the expected strain rate dependencies of the pressure, energy and shear viscosity. For the first time, the pressure is convincingly observed to vary linearly with an apparent analytic y2 dependence, in contrast to the predicted y3/2 dependence of mode -coupling theory. Our best extrapolation of the zero -shear viscosity for argon gives excellent agreement (within 1%) with the known experimental data. To the best of our knowledge, this the first time that such accuracy has been achieved with NEMD simulations. This encourages performing simulations with accurate potentials for transport properties.

<p>There are many different codes available for making molecular dynamic simulation. Most of these are focused on high performance mainly. We have moved that focus towards modularity, flexibility and user friendliness. Our goal has been to design a software that is easy to use, can handle many different kind of simulations and is easily extendable to meet new requirements.</p><p>In the report we present you with the theory that is needed to understand the principles of a molecular dynamics simulation. The four different potentials we have used in the software are presented. Further we give a detailed description of the design and the different design choices we have made while constructing the software.</p><p>We show some examples of how the software can be used and discuss some aspects of the performance of the implementation. Finally we give our thoughts on the future of the software.</p>

<p>In the present work, molecular dynamics simulations were used to evaluate the molecular interactions in prepolymerization mixtures, as occurring during production of molecularly imprinted polymers. The systems simulated were produced based on earlier studies for reference of results. Four systems were simulated in order to investigate the effect on molecular interactions based upon the choice of porogen (acetonitrile or chloroform) and proton transfers. The systems consisted of phenylalanine anilide as template, methacrylic acid as functional monomer, ethylene glycol dimethacrylate as crosslinker and 2,2’-azobis-(2-methylpropionitrile) as radical initiator, with either acetonitrile or chloroform as porogen. Trajectories from the simulations were evaluated through radial distribution function analysis, grid density analysis and hydrogen bond analysis to investigate molecular interactions and complex formations in the simulated complete prepolymerization mixtures. Focus was on functional monomer-template, crosslinker-template and template-template complex formations. The results showed that the porogen influences molecular interactions in complete prepolymerization mixtures. Formation of higher order complexes was confirmed in all of the systems involving all of the investigated molecular species in the prepolymerization mixtures. The results could also confirm the presence of previously observed complexes between functional monomer and template (2:1 and 1:1 stoichiometry) and the prevalence of template dimerization, as well as a high involvement of crosslinker in complex formation.</p>

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

Computer simulations play a profound and fundamental role inmodern theoretical physics, chemistry and materials science. Tounderstand the complex physics of metally liquids, metals,quasicrystals and metally glasses a working model imposing thelocal and global order is needed. Experiments and theory havepredicted the local order in liquid metals to beicosahedral. The current work has been done using molecular dynamicscomputer simulations of a monatomic system using a simplepair-potential for the interactions. Two new pair-potentialshas been developed, the Zetterling-1(Z1) and Zetterling-2(Z2)potentials. They are specifically modeled to impose icosahedralorder. The basis for the development of the potentials was theold Dzugutov potential which is known to freeze into adodecagonal quasicrystal. The new Zetterling potentials have alonger interaction range and a narrower first minimum. The morenarrow first minimum will enhance the local icosahedralordering and the longer interaction range was introduced toincorporate a second maximum in the potential mimicing theFriedel oscillations found in metallic systems. These Friedeloscillations are due to the singularity which arises at theFermi surface due to the screening of the positive charge bythe electron gas. Five papers are included in the study. The first two papersare studies of icosahedral clustering in the liquid andsupercooled liquid. The simulations in Paper I was done usingthe old Dzugutov potential while the new potentials were usedin Paper II using both molecular dynamics and the Basin Hoppingalgorithm presented in Chapter 5. Paper III considers theconcept of dynamical ergodicity in the context of thesuper-cooled liquid behaviour. The simulations were made usingthe old Dzugutov potential. Paper IVr eports a moleculardynamics simulation using the Dzugutov potential undersuper-cooling. A formation of icosahedrally structured domainswith distinctly slow diffusion which grows with cooling in alow-dimensional manner and percolate around Tc, the criticaltemperature of the mode-coupling theory. A sharp slowing downof the structural relaxation relative to diffusion is observed.It is concluded that this effect cannot be accounted for by thespatial variation in atomic mobility. The low-dimensionalclustering is discussed as a possible mechanism of fragility.Paper Vin vestigates the crystallization of a simple monatomicliquid model which utilizes the Zetterling-1 potential. Thesystem forms a thermodynamically stable solid phase exhibitingcubic symmetry. Its diffraction pattern is identified as thatof γ-brass, a tetrahedrally packed crystalline structurewith 52 atoms in the unit cell. <b>Keywords:</b>simple liquids, molecular dynamics, pairpotential, icosahedral cluster.

This thesis consists of the four papers which consider different aspects of stochastic process modeling, error analysis, and minimization of computational cost.      In Paper I, we construct a Multipath Fading Channel (MFC) model for wireless channels with noise introduced through scatterers flipping on and off. By coarse graining the MFC model a Gaussian process channel model is developed. Complexity and accuracy comparisons of the models are conducted.      In Paper II, we generalize a multilevel Forward Euler Monte Carlo method introduced by Mike Giles for the approximation of expected values depending on solutions of Ito stochastic differential equations. Giles' work proposed and analyzed a Forward Euler Multilevel Monte Carlo (MLMC) method based on realizations on a hierarchy of uniform time discretizations and a coarse graining based control variates idea to reduce the computational cost required by a standard single level Forward Euler Monte Carlo method. This work is an extension of Giles' MLMC method from uniform to adaptive time grids. It has the same improvement in computational cost and is applicable to a larger set of problems.      In paper III, we consider the problem to estimate the mean of a random variable by a sequential stopping rule Monte Carlo method. The performance of a typical second moment based sequential stopping rule is shown to be unreliable both by numerical examples and by analytical arguments. Based on analysis and approximation of error bounds we construct a higher moment based stopping rule which performs more reliably.      In paper IV, Born-Oppenheimer dynamics is shown to provide an accurate approximation of time-independent Schrödinger observables for a molecular system with an electron spectral gap, in the limit of large ratio of nuclei and electron masses, without assuming that the nuclei are localized to vanishing domains. The derivation, based on a Hamiltonian system interpretation of the Schrödinger equation and stability of the corresponding hitting time Hamilton-Jacobi equation for non ergodic dynamics, bypasses the usual separation of nuclei and electron wave functions, includes caustic states and gives a different perspective on the Born-Oppenheimer approximation, Schrödinger Hamiltonian systems and numerical simulation in molecular dynamics modeling at constant energy. / <p>QC 20120508</p>

Computational research making use of molecular dynamics (MD) simulations has begun to expand the paradigm of structural biology to include dynamics as the mediator between structure and function. This work aims to expand the utility of MD simulations by developing Principal Component Analysis (PCA) techniques to extract the biologically relevant information in these increasingly complex data sets. Gramicidin is a simple protein with a very clear functional role and a long history of experimental, theoretical and computational study, making it an ideal candidate for detailed quantitative study and the development of new analysis techniques. First we quantify the convergence of our PCA results to underwrite the scope and validity of three 64 ns simulations of gA and two covalently linked analogs (SS and RR) solvated in a glycerol mono-oleate (GMO) membrane. Next we introduce a number of statistical measures for identifying regions of anharmonicity on the free energy landscape and highlight the utility of PCA in identifying functional modes of motion at both long and short wavelengths. We then introduce a simple ansatz for extracting physically meaningful modes of collective dynamics from the results of PCA, through a weighted superposition of eigenvectors. Applied to the gA, SS and RR backbone, this analysis results in a small number of collective modes which relate structural differences among the three analogs to dynamic properties with functional interpretations. Finally, we apply elements of our analysis to the GMO membrane, yielding two simple modes of motion from a large number of noisy and complex eigenvectors. Our results demonstrate that PCA can be used to isolate covariant motions on a number of different length and time scales, and highlight the need for an adequate structural and dynamical account of many more PCs than have been conventionally examined in the analysis of protein motion.

When evaluating integration schemes used in molecular dynamics (MD) simulations, energy conservation is often cited as the primary criterion by which the integrators should be com- pared. As a result variable stepsize Runge-Kutta methods are often ruled out of consideration due to their characteristic energy drift. We have shown that by appropriately modifying the stepsize selection strategy in a variable stepsize RK method it is possible for the MD practitioner to obtain substantial control over the energy drift during the course of a simulation. This ability has been previously unreported in the literature, and we present numerical examples to illustrate that it can be achieved without sacrificing computational efficiency under currently obtainable timescales.