| 1. |
- Harczuk, Ignat, 1987-
(författare)
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Atomic decomposition of molecular properties
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis, new methodology of computing properties aimed for multipleapplications is developed. We use quantum mechanics to compute propertiesof molecules, and having these properties as a basis, we set up equations basedon a classical reasoning. These approximations are shown to be quite good inmany cases, and makes it possible to calculate linear and non-linear propertiesof large systems.The calculated molecular properties are decomposed into atomic propertiesusing the LoProp algorithm, which is a method only dependent on the overlapmatrix. This enables the expression of the molecular properties in the two-site atomic basis, giving atomic, and bond-centric force-fields in terms of themolecular multi-pole moments and polarizabilities. Since the original LoProptransformation was formulated for static fields, theory is developed which makesit possible to extract the frequency-dependent atomic properties as well. Fromthe second-order perturbation of the electron density with respect to an externalfield, LoProp is formulated to encompass the first order hyperpolarizability.The original Applequist formulation is extended into a quadratic formula-tion, which produces the second-order shift in the induced dipole moments of thepoint-dipoles from the hyperpolarizability. This enables the calculation of a to-tal hyperpolarizability in systems consisting of interacting atoms and molecules.The first polarizability α and the first hyperpolarizability β obtained via theLoProp transformation are used to calculate this response with respect to anexternal field using the quadratic Applequist equations.In the last part, the implemented analytical response LoProp procedureand the quadratic Applequist formalism is applied to various model systems.The polarizable force-field that is obtained from the decomposition of the staticmolecular polarizability α is tested by studying the one-photon absorption spec-trum of the green fluorescent protein. From the frequency dispersion of thepolarizability α(ω), the effect of field perturbations is evaluated in classicaland QM/MM applications. Using the dynamical polarizabilities, the Rayleigh-scattering of aerosol clusters consisting of water and cis–pinonic acid moleculesis studied. The LoProp hyperpolarizability in combination with the quadraticApplequist equations is used to test the validity of the model on sample wa-ter clusters of varying sizes. Using the modified point-dipole model developedby Thole, the hyper-Rayleigh scattering intensity of a model collagen triple-helix is calculated. The atomic dispersion coefficients are calculated from thedecomposition of the real molecular polarizability at imaginary frequencies. Fi-nally, using LoProp and a capping procedure we demonstrate how the QM/MMmethodology can be used to compute x-ray photoelectron spectra of a polymer.
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| 2. |
- Kubyshkina, Elena, 1990-
(författare)
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Ab initio modelling of interfaces in nanocomposites for high voltage insulation
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Dielectric nanocomposite materials have been experimentally proven to have properties that are beneficial in applications for efficient energy transport. However, today there are still no empirical models or rules that can predict the performance of a certain combination of materials in the nanocomposite, and there are also no definitive explanations of their dielectric behavior. A deeper understanding of the phenomena behind these materials' response to an applied electric field can open new possibilities for improvement of the insulating properties of nanocomposites.The goal of this work is to locate the key processes that are responsible for dielectric performance. The methodology of the study is based on ab initio technology, that relies solely on the knowledge of chemical and structural composition of the material. In this work, the charge-related properties of nanocomposite interfaces are studied. The primary material of the study is chosen to be polyethylene-based composite with magnesium oxide nanoparticles.The impact of the nanoparticle crystal surface termination and its silane treatment on the electronic structure of the interface between MgO and polyethylene are investigated here. Moreover, the effects of presence of carboxyl defect and water molecule near the interface are considered in this work as well.Based on the calculated electronic structure data, a model for charge dynamics is proposed. The model explains mechanisms for conductivity and space charge reduction in nanocomposites, but also predicts an increase in thermal stress and susceptibility for chemical defects. It is suggested here that the suppression mechanisms for space charge and conductivity in nanocomposites are inherently unstable and can also accelerate material aging.
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| 3. |
- Blust, Kelly, et al.
(författare)
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Integration of stem cell-derived pancreatic aggregates into FN-silk network for in vitro cultivation and in vivo transplantation
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Type 1 diabetes is a life-threatening disease characterized by lifelong insulin dependency and a reduced quality of life. Pancreatic islet transplantation is a promising treatment but is limited by donor shortages and significant islet loss during the procedures. The usage of pancreatic islet-like aggregates derived from pluripotent stem cells (SC-islets) could solve the problem of shortage of islets. Incorporating these SC-islets into a supporting scaffold could protect them during handling.FN-silk, a recombinantly produced spider silk protein functionalized with a cell adhesion motif from fibronectin, can generate 3D networks that mimic the extracellular matrix (ECM). We herein demonstrate a reproducible method for integrating SC-islets well-distributed within stable 3D networks of FN-silk. These SC-islets showed high viability and maintained functionality, with increased glucagon expression and improved beta cell maturation as compared to free SC-islets. Additionally, the support of FN-silk networks enables cultivation of SC-islets under conditions needed for scale-up. Moreover, the integration of the SC-islets into sheets of FN-silk networks facilitates handling during transplantation into the anterior chamber of the eye (ACE) of rabbits. Such transplanted FN-silk incorporated SC-islets were found vascularized six weeks post-transplantation, with sustained insulin and glucagon expression.
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| 4. |
- Sjöqvist, Jonas, 1985-
(författare)
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Light interactions in flexible conjugated dyes
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis methodological developments have been made for the description of flexible conjugated dyes in room temperature spectrum calculations.The methods in question target increased accuracy and efficiency by combining classical molecular dynamics (MD) simulations with time-dependent response theory spectrum calculations. For absorption and fluorescence spectroscopies a form of conformational averaging is used, where the final spectrum is obtained as an average of spectra calculated for geometries extracted from ground and excited state MD simulations. For infrared and Raman spectroscopies averaged spectra are calculated based on individual spectra, obtained for zero-temperature optimized molecular structures, weighted by conformational statistics from MD trajectories. Statistics for structural properties are also used in both cases to gain additional information about the systems, allowing more efficient utilization of computational resources. As it is essential that the molecular mechanics description of the system is highly accurate for methods of this nature to be effective, high quality force field parameters have been derived, describing the molecules of interest in either the MM3 or CHARMM force fields.These methods have been employed in the study of three systems. The first is a platinum(II) actylide chromophore used in optical power limiting materials, for which a ultraviolet/visible absorption spectrum has been calculated. The second is a family of molecular probes called luminescent conjugated oligothiophenes, used to detect and characterize amyloid proteins, for which both absorption and fluorescence spectra have been calculated. Finally, infrared and Raman spectra have been calculated for a group of branched oligothiophenes used in organic solar cells.In addition, solvation effects have been studied for conjugated poly\-eletrolytes in water, resulting in the development of two solvation models suitable for this class of molecules. The first uses a quantum meachanics/molecular mechanics (QM/MM) description, in which the solute mole\-cule is described using accurate quantum mechanical methods while the surrounding water molecules are described using point charges and polarizable point dipoles. The second discards the water entirely and removes the ionic groups of the solute. The QM/MM model provides highly accurate results while the cut-down model gives results of slightly lower quality but at a much reduced computational cost.Finally, a study of protein-dye interactions has been performed, with the goal of explaining changes in the luminescence properties of the LCO chromophores when in the presence of amyloid proteins. Results were less than conclusive.
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