Two force fields, the GROMOS53A5/53A6 (united atom) and the AMBER95 (all atom) parameter sets, coupled with partial atomic charges derived from quantum mechanical calculations were evaluated for their ability to reproduce the known crystalline forms of the polyols mannitol and sorbitol. The force fields were evaluated using molecular dynamics simulations at 10 K (which is akin to potential energy minimization) with the simulation cell lengths and angles free to evolve. Both force fields performed relatively poorly, not being able to simultaneously reproduce all of the crystal structures within a 5% deviation level. The parameter sets were then systematically optimized using sensitivity analysis, and a revised AMBER95 set was found to reproduce the crystal structures with less than 5% deviation from experiment. The stability of the various crystalline forms for each of the parameter sets (original and revised) was then assessed in extended MD simulations at 298 K and 1 bar covering 1 ns simulation time. The AMBER95 parameter sets (original and revised) were found to be effective in reproducing the crystal structures in these more stringent tests. Remarkably, the performance of the original AMBER95 parameter set was found to be slightly better than that of the revised set in these simulations at 298 K. The results of this study suggest that, whenever feasible, one should include molecular simulations at elevated temperatures when optimizing parameters. / Dutch Top Institute Pharma

The dynamic properties of Palladium (Pd) and Aluminum (Al) metals and their alloys are investigated by means of Molecular Dynamics using the Quantum Sutton-Chen force field in five different concentrations. Calculations have been carried out for liquid structures. Although this study is done for liquid structures, basic solid state properties are also investigated to prove the validity of potential parameters. Results are compared with each other and with experimental, theoretical and simulated results. Liquid state transferability of Quantum Sutton-Chen parameters have been investigated and discussed. High temperature properties, which are not easy to work experimentally, are simulated and high temperature behavior of Pd-Al alloy is investigated.

In this thesis, issues pertaining to the dynamics of nanoscale liquid systems, such as nanojets and nanobridges, in vacuum as well as in ambient gaseous conditions, are explored using both extensive molecular dynamics simulations and theoretical analyses. The simulation results serve as ``theoretical experimental data' (together with laboratory experiments when available) for the formulation, implementation, and testing of modified hydrodynamic formulations, including stochastic hydrodynamics. These investigations aim at extending hydrodynamic formulations to the nanoscale regime. In particular, the instability, and breakup of liquid nanobridges and nanojets are addressed in details. As an application of the microscopic hydrodynamics, a heated-nozzle technique to generate and control nanojets is proposed. Both simulations and microscopic hydrodynamic modeling reveal the formation of a ``virtual convergent nozzle', which consists of a narrowing convergent liquid core within a growing evaporative sheath, by the nanojet itself inside the real nozzle. The diameter of the resulting ejected nanojet is much smaller than the diameter of the nozzle. By adjusting the temperature distribution of the real nozzle, the size and shape of the virtual nozzle are changed, which in turn changes the diameter and the direction of the ejected nanojet.

Computational tools play an important role in the description of biological systems. Scientists describe and study structure, conformational changes and interactions between molecules in silico, often as a cheaper and faster alternative for biosynthesis. The simulated dynamic behavior in time of a molecular system is a straight forward source of information about substrate-enzyme interactions at the atomic level, and a powerful tool for the identification of molecular properties important in enzymatic reactions. Our study is focused on the computational investigation of structure and substrate specificity of hydrolases important in biotransformation. The computational work was performed in close collaboration with biochemists-experimentalists from Charles University and the Microbiological Institute of the Academy of Sciences of the Czech Republic. Hydrolases have great a potential in the chemoenzymatic synthesis of modified carbohydrates with regulated properties. Carbohydrates, as substrates of hydrolases, are important in normal functionality of many organisms. They have a dual role in immune response regulation: some carbohydrates (like GlcNAc and ManNAc) participate in activation and some (like GalNAc) in suppressing immunity; glycosidase deficiency is associated with a number of lysosomal disorders. We used homology modeling, computational docking and molecular dynamics simulation (MD) methods for the complex study of fungal hydrolases: alpha-galactosidase/alpha-N-acetylgalactosaminidase from Aspergillus niger; beta-N-acetylhexosaminidases (HEX) (from Aspergillus oryzae and Penicillium oxalicum); nitrilase from Aspergillus niger. Our structural study unambigously demonstrates that the enzyme encoded by genes variant A (aglA) from A. niger is able to accept alpha-N-acetylgalactosamine as its substrate and explains structural features responsible for its specificity. Homology models of HEXs from P. oxalicum and A. oryzae were built and compared. Homology models were used to study the role of protein glycosylation, disulfide bonds, dimer formation and interaction with natural and modified substrates. Model of nitrilase from Aspergillus niger helped to analyze multimer formation.

abstract: A comprehensive and systematic investigation on the diffusion and phase behaviors of nanoparticles and macromolecules in two component liquid-liquid systems via Molecule Dynamic (MD) simulations is presented in this dissertation. The interface of biphasic liquid systems has attracted great attention because it offers a simple, flexible, and highly reproducible template for the assembly of a variety of nanoscale objects. However, certain important fundamental issues at the interface have not been fully explored, especially when the size of the object is comparable with the liquid molecules. In the first MD simulation system, the diffusion and self-assembly of nanoparticles with different size, shape and surface composition were studied in an oil/water system. It has been found that a highly symmetrical nanoparticle with uniform surface (e.g. buckyball) can lead to a better-defined solvation shell which makes the “effective radius” of the nanoparticle larger than its own radius, and thus, lead to slower transport (diffusion) of the nanoparticles across the oil-water interface. Poly(N-isopropylacrylamide) (PNIPAM) is a thermoresponsive polymer with a Lower Critical Solution Temperature (LCST) of 32°C in pure water. It is one of the most widely studied stimulus-responsive polymers which can be fabricated into various forms of smart materials. However, current understanding about the diffusive and phase behaviors of PNIPAM in ionic liquids/water system is very limited. Therefore, two biphasic water-ionic liquids (ILs) systems were created to investigate the interfacial behavior of PNIPAM in such unique liquid-liquid interface. It was found the phase preference of PNIPAM below/above its LCST is dependent on the nature of ionic liquids. This potentially allows us to manipulate the interfacial behavior of macromolecules by tuning the properties of ionic liquids and minimizing the need for expensive polymer functionalization. In addition, to seek a more comprehensive understanding of the effects of ionic liquids on the phase behavior of PNIPAM, PNIPAM was studied in two miscible ionic liquids/water systems. The thermodynamic origin causes the reduction of LCST of PNIPAM in imidazolium based ionic liquids/water system was found. Energy analysis, hydrogen boding calculation and detailed structural quantification were presented in this study to support the conclusions. / Dissertation/Thesis / Doctoral Dissertation Chemical Engineering 2017

京都大学 / 新制・論文博士 / 博士(理学) / 乙第13434号 / 論理博第1576号 / 新制||理||1682(附属図書館) / 京都大学大学院理学研究科 / (主査)教授 谷村 吉隆, 教授 林 重彦, 教授 渡邊 一也 / 学位規則第4条第2項該当 / Doctor of Science / Kyoto University / DGAM

<div>Organic mixed ion-electron conducting (OMIEC) polymers are capable of transporting both electrons and ions. This unique functionality underpins many emerging applications, including biosensors, electrochemical transistors, and batteries. The fundamental operating principles and structure-function relationships of OMIECs are still being investigated. Computational tools such as coarse-grained molecular dynamics (CGMD), which use simpler representations than in atomistic modeling, are ideal to study OMIECs, as they can explore the slow dynamics and large length scale features of polymers. Nevertheless, methods development is still required for CGMD simulations to accurately describe OMIECs.</div><div><br></div><div>In this thesis, two CGMD simulation approaches have been adopted. One is a so-called "top-down" approach to develop a generic model of OMIECs. Top-down models are phenomenological but capable of exploring a broad space of materials variables, including backbone anisotropy, persistence length, side-chain density, and hydrophilicity. This newly developed model was used to interrogate the effect of side-chain polarity and patterning on OMIEC physics. These studies reproduce experimentally observed polymer swelling while for the first time clarifying several molecular factors affecting charge transport, including the role of trap sites, polaron delocalization, electrolyte percolation, and suggesting side-chain patterning as a potential tool to improve OMIEC performance.</div><div><br></div><div>The second strategy pursued in this thesis is bottom-up CGMD modeling of specific atomistic systems. The bottom-up approach enables CGMD simulations to be quantitatively related to specific materials; yet, the sources of error and methods for addressing them have yet to be systematically established. To address this gap, we have studied the effect of the CG mapping operator, an important CG variable, on the fidelity of atomistic and CGMD simulations. A major observation from this study is that prevailing CGMD methods are underdetermined with respect to atomistic training data. In a separate study, we have proposed a hybrid machine-learning and physics-based CGMD framework that utilizes information from multiple sources and improves on the accuracy of ML-only bottom-up CGMD approaches. </div>

Membranes made of composite polymer material are widely employed to separate gas mixtures in industrial processes. These membranes have better performance than membranes consisting of polymer alone. To understand the mechanism and therefore aid membrane design it is essential to explore the penetrant transport in the complex composites from the molecular level, but few researchers have done such research to our knowledge. Herein the penetrant transport in the composite Poly (4-methyl-2-pentyne) (PMP) and silica nanoparticle is being explored with molecular dynamics (MD) simulations. The structure of the PMP and amorphous silica nanoparticle composite was modeled and with the structure the variation of the cavity size distribution was established due to the existence of nanoparticles. The diffusivity of different penetrants, including H2, O2, Ar, CH4 and n-C4H10 was determined through least square fit of the data of mean square displacement at different times in the Fickian diffusive regime. The solubility coefficients and the permeability of different penetrants in PMP and the composite were calculated and the distribution of potential difference due to the penetrant insertion was analyzed in detail to find the reason of higher solubility in composite than pure PMP. Silica has different crystalline form. In faujasite silica, there are pores that are large enough to allow penetrants to pass through, while in cristobalite silica, the Si and O atoms are densely packed and there are no pores that penetrants can pass through. The transport properties of penetrants in the composite of PMP and nanoparticles of these two types of silica are therefore different. The molecular dynamics method was employed in the research to explore the transport of different penetrants in the composites of PMP and nanoparticles of two forms of silica, namely the cristobalite form and the faujasite form. The structures of the PMP and nanoparticle of cristobalite silica composite (PMPC) and the PMP and nanoparticle of faujasite silica composite (PMPF) were established and relaxed. With the relaxed structure, the cavity size change due to the insertion of both types of nanoparticle was analyzed. The diffusivity of different penetrants was determined through least square fit of the data of mean square displacement at different time in Fickian diffusive regime. The solubility coefficients and the permeability of different penetrants in PMPC and PMPF were calculated and compared. The parameters of "Ti" in the Lennard-Jones potential equation were estimated; MD simulation of penetrants transport in composite poly (4-methyl-2-pentyne) and TiO2 nanoparticles were done; the simulation results were compared with composite poly (4-methyl-2-pentyne) and silica nanoparticles. / Ph. D.

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Nuclear Engineering, 1982. / MICROFICHE COPY AVAILABLE IN ARCHIVES AND SCIENCE. / Includes bibliographical references. / by Francisco Javier Carrion. / M.S.

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Nuclear Engineering, 1982. / MICROFICHE COPY AVAILABLE IN ARCHIVES AND SCIENCE. / Includes bibliographical references. / by Khaled Awni Touqan. / Ph.D.