In this dissertation, we construct a temperature controlled sample stage that is compatible with high numerical aperture objective optical microscope, and perform single molecule experiments under the system. Mixing dilute fluorophore (CdSe/ZnS quantum dot, DiI, Rhodamine B) into the liquid crystal matrix (5CB), we monitor the fluorescence dynamics of the individual fluorophore at various temperature. Different from the thermodynamic states of conventional materials, those specific class of materials which we called ¡§liquid crystals¡¨ are attracted for their existence of unique liquid crystal phase, which exhibits a solid-state like higher orientation ordering, and a liquid-state like liquidity. Probe individual fluorophore allows us to monitor the nanometer length scale local structural and dynamic heterogeneity in the solid, liquid crystal and liquid phases. The operating temperature of the platform covers more than 20 oC to 40 oC range with stability much better than 0.1 oC. Quantum dot in PMMA exhibits a clear on-off blinking behavior, and the single exponential fluorescence lifetime relaxation. While in the solid phase of the liquid crystal matrix, quantum dot exhibits similar behavior, which indicates the quantum dot is confined in the matrix. However, there exists slightly difference in decay lifetime. On the contrary, in the liquid crystalline phase as well as the liquid phase, quantum dot exhibits bi-exponential relaxation behavior. Besides a similar time scale relaxation dynamics, there exists additional fast decay behavior, which is from the feasible rotational rotation in the non-rigid matrix. In particular, the anisotropic decay dynamics in the liquid crystalline phase indicates the orientation preference of the liquid crystal molecules. Fluorescence Correlation Spectroscopy (FCS) provides the information of local dynamics of various time scales. FCS results exhibit an unclear transition that crossovers several decades in time scale, which indicates the highly heterogeneity of the liquid crystal. The results of DiI exhibits different rising time in the fluorescence lifetime measurement, which implies the forming of aggregation due to the limited solubility of the DiI molecules in the liquid crystal matrix. Results of Rhodamine B exhibit a clear rotational diffusion dynamics at ~ microsecond scale and the corresponding translational diffusion dynamics at ~ mini-second scale. Moreover, the transition time scale of translational diffusion exhibits a temperature dependence. At higher temperature, it shifts to a shorter time scale.

Using statistical physics principles to solve problems in biology is one of the most promising directions due to the complexity and non-equilibrium fluctuations in biological systems. In this work, we try to describe the dynamics at both cellular and molecular levels. Microtubule dynamics and dynamic disorder of enzyme proteins are two of the examples we investigated. The dynamics of microtubules and the mechanical properties of these polymers are essential for many key cellular processes. However, critical discrepancies between experimental observations and existing models need to be resolved before further progress towards a complete model can be made. We carried out computational studies to compare the mechanical properties of two alternative models, one corresponding to the existing, conventional model, and the other considering an additional type of tubulin lateral interaction described in a cryo-EM structure of a proposed trapped intermediate in the microtubule assembly process. Our work indicates that a class of sheet structures is transiently trapped as an intermediate during the assembly process in physiological conditions. In the second part of the work, we analyzed enzyme slow conformational changes in the context of regulatory networks. A single enzymatic reaction with slow conformational changes can serve as a basic functional motif with properties normally discussed with larger networks in the field of systems biology. The work on slow enzyme dynamics fills the missing gap between studies on intramolecular and network dynamics. We also showed that enzyme fluctuations could be amplified into fluctuations in phosphorylation networks. This can be used as a novel biochemical "reporter" for measuring single enzyme conformational fluctuation rates. / Ph. D.

abstract: Charge transport in molecular systems, including DNA (Deoxyribonucleic acid), is involved in many basic chemical and biological processes. Studying their charge transport properties can help developing DNA based electronic devices with many tunable functionalities. This thesis investigates the electric properties of double-stranded DNA, DNA G-quadruplex and dsDNA with modified base. First, double-stranded DNA with alternating GC sequence and stacked GC sequence were measured with respect to length. The resistance of DNA sequences increases linearly with length, indicating a hopping transport mechanism. However, for DNA sequences with stacked GC, a periodic oscillation is superimposed on the linear length dependence, indicating a partial coherent transport. The result is supported by the finding of delocalization of the highest occupied molecular orbitals of Guanines from theoretical simulation and by fitting based on the Büttiker’s theory. Then, a DNA G4-duplex structures with a G-quadruplex as the core and DNA duplexes as the arms were studied. Similar conductance values were observed by varying the linker positions, thus a charge splitter is developed. The conductance of the DNA G-tetrads structures was found to be sensitive to the π-stacking at the interface between the G-quadruplex and DNA duplexes by observing a higher conductance value when one duplex was removed and a polyethylene glycol (PEG) linker was added into the interface. This was further supported by molecular dynamic simulations. Finally, a double-stranded DNA with one of the bases replaced by an anthraquinone group was studied via electrochemical STM break junction technique. Anthraquinone can be reversibly switched into the oxidized state or reduced state, to give a low conductance or high conductance respectively. Furthermore, the thermodynamics and kinetics properties of the switching were systematically studied. Theoretical simulation shows that the difference between the two states is due to a difference in the energy alignment with neighboring Guanine bases. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2016

This dissertation discusses the Landau-Zener (LZ) theory and its application in noisy environments and in many-body systems. The first project considers the effect of fast quantum noise on LZ transitions. There are two important time intervals separated by the characteristic LZ time. For each interval we derive and solve the evolution equation, and match the solutions at the boundaries to get a complete solution. Outside the LZ time interval, we derive the master equation, which differs from the classical equation by a quantum commutation term. Inside the LZ time interval, the mixed longitudinal-transverse noise correlation renormalizes the LZ gap and the system evolves according to the renormalized LZ gap. In the extreme quantum regime at zero temperature our theory gives a beautiful result which coincides with that of other authors. Our initial attempts to solve two experimental puzzles - an isotope effect and the quantized hysteresis curve of a single molecular magnet - are also discussed. The second project considers an ultracold dilute Fermi gas in a magnetic field sweeping across the broad Feshbach resonance. The broad resonance condition allows us to use the single mode approximation and to neglect the energy dispersion of the fermions. We then propose the Global Spin Model Hamiltonian, whose ground state we solve exactly, which yields the static limit properties of the BEC-BCS crossover. We also study the dynamics of the Global Spin Model by converting it to a LZ problem. The resulting molecular production from the initial fermions is described by a LZ-like formula with a strongly renormalized LZ gap that is independent of the initial fermion density. We predict that molecular production during a field-sweep strongly depends on the initial value of magnetic field. We predict that in the inverse process of molecular dissociation, immediately after the sweeping stops there appear Cooper pairs with parallel electronic spins and opposite momenta.

Magnetism of carbon-based materials is a challenging area for both fundamental research and possible applications. We present studies of low-dimensional carbon-based magnetic systems (fullerene-diluted molecular magnets, carbon nanotubes, graphite fluoride, and nanoporous carbon) by means of SQUID magnetometer, X-ray diffraction and vibrational spectroscopy, the latter techniques used as complementary instruments to find a correlation between the magnetic behaviour and the structure of the samples.In the first part of the thesis, characteristic features of the magnetization process in aligned films of carbon nanotubes with low concentration of iron are discussed. It is shown that the magnetism of such structures is influenced by quantum effects, and the anisotropy behaviour is opposite to what is observed in heavily doped nanotubes.In the second part, Mn12-based single molecular magnets with various carboxylic ligands and their 1:1 fullerene-diluted complexes are studied. We prove that magnetic properties of such systems strongly depend on the environment, and, in principle, it is possible to design a magnet with desirable properties. One of the studied compounds demonstrated a record blocking temperature for a single molecular magnet. Both fullerene-diluted complexes demonstrated “magnetization training” effect in alternating magnetic fields and the ability to preserve magnetic moment.The third and the fourth parts of the thesis are dedicated to the analysis of various contributions to the magnetic susceptibility of metal-free carbon-based systems – intercalated compounds of graphite fluorides and nanoporous oxygen-eroded graphite. The magnetic properties of these systems are strongly dependent on structure, and can be delicately tuned by altering the π-electron system of graphite, i. e. by degree of fluorination of intercalated compounds and by introduction of boron impurity to the host matrix of nanoporous graphite. / Magnetism av kolbaserade material är ett utmanande område för både grundforskning och möjliga tillämpningar. Vi presenterar studier med låg-dimensionella kolbaserade magnetiska system (fulleren-utspädda molekylära magneter, kolnanorör, grafit fluorid och nanoporösa kol) med hjälp av SQUID magnetometer, röntgendiffraktion och vibrerande spektroskopi, de senare tekniker som används som komplement instrument för att finna sambandet mellan den magnetiska uppträdande och strukturen hos proven. I den första delen av avhandlingen är egenheter från magnetisering processen i linje filmer av kolnanorör med låg koncentration av järn diskuteras. Det visas att magnetism av sådana strukturer påverkas av kvantmekaniska effekter och anisotropin beteende är motsatsen till vad som observerats i kraftigt dopade nanorör. I den tvåa delen är Mn12-baserade enda-molekyl magneter med olika karboxylsyror ligander och deras 1:1 fulleren-utspädda komplex studeras. Vi visar att magnetiska egenskaperna hos sådana system beror i hög grad på miljön, och i princip är det möjligt att utforma en magnet med önskvärda egenskaper. En av de studerade föreningarna visade en post blockeringstemperaturen för en enda molekylär magnet. Både fulleren-utspädda komplex visade "magnetisering utbildning" effekt i alternerande magnetfält och möjligheten att bevara magnetiskt moment. Den tredje och fjärde delarna av avhandlingen är avsedda för inneboende magnetism av analys av olika bidrag till magnetisk susceptibilitet av metall-fritt kol-baserade system -inskjutna föreningar grafit fluorider och nanoporösa O2-eroderade grafit. Magnetiska egenskaperna hos dessa system är starkt beroende av strukturen, och kan fint avstämmas genom att man ändrar π-elektronsystem av grafit, i. e. med graden av fluorering av inskjutna föreningar och genom införandet av bor föroreningar till värd matris av nanoporösa grafit.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The preparation of semiconductor nanocrystals (SNC) has been reported as the research foccus in several works owing to the optical and luminescent properties as well as the broad fields of application. In the first stage of this work, 2-mercaptoethanol-capped ZnS nanocrystals were prepared and characterized. The resulting nanocrystals were incorporated into a pre-formed polyurethane matrix playing the role of polyol-type monomer. In the second stage,the ZnS nanocrystals were doped with Mn2+ cations, considering that this strategy may improve the optical properties of the nanocrystals. In this study, it was observed that the changes in experimental parameters may allow the controlled formation of ZnO instead of ZnS, introducing a new route to ZnO obtainment. Concentration values of Mn2+ were lower than 1 %. Moreover, a study was carried out in order to clarify the structure-property relation, observing that the substitution of Zn2+ ions by Mn2+ ones may influence the optical properties of ZnO. From characterization data, the formation of ZnO was confirmed and it became clear that dissolving or notpreviously the capping agent in water was the key factor for the formation of ZnO instead of ZnS.Since small dopant concentrations lead to interesting results for ZnO, the same conditions were used to study the doping of ZnS in the third stage. This lead, however, to self-assembly of nanocrystals into nanowires after the doping process. Self-assembly did not cause changes in the absorption energies according to UV/visible spectra.This was the case even when the dopant concentration in the ZnS nanocrystals increased, as analyzed by atomic absorption spectrometry. On the other hand, emission spectra were sensitive to changes in Mn2+ concentration, showing a behavior consistent with increases in point defects such as sulfur vacancies and interstitial sulfur. It was evidenced that Mn2+ ions are presente in the ZnS structure.The last study reveals a novel supramolecular arrangement of the crystalline structure of a zinc-thiosemicarbazone complex [Zn(TPTSC)2], which exhibits potentiality as a single-source molecular precursor to ZnS nanocrystals in future works. / A preparação de nanocristais semicondutores (NCS) tem sido objeto de pesquisa devido às propriedades ópticas de luminescência que apresentam e à ampla área de aplicação. Na primeira etapa deste trabalho foram preparados nanocristais de ZnS passivados com 2-mercaptoetanol (ME) e caracterizados. Os nanocristais obidos foram incorporados em uma matriz polimérica pré-formada funcionando como um precursor do tipo poliol. Na segunda etapa, uma vez que as propriedades ópticas podem ser melhoradas com a dopagem dos nanocristais, os mesmos foram dopados com Mn2+, porém uma modificação na parte experimentalà levou a formação controladade ZnO no lugar de ZnS, introduzindo uma nova rota para a obtenção de ZnO. Os valores das concentrações de Mn2+utilizadas foram inferiores a 1%. Além disso, foi feito um estudo para correlacionar a estrutura-propriedade no qual foi observado que a substituição dos íons Mn2+ pelos íons Zn2+ influencia as propriedades ópticas do ZnO. Através das caracterizações, ficou confirmada a formação do ZnO e que a forma com a qual o passivante foi adicionado ao sistema favorecia a formação de ZnS (quando o passivante foi adicionado diretmente) e de ZnO (quando feita uma solução aquosa do passivante). Como pequenas concentrações do dopante conduziram a resultados interessantes para o ZnO, os mesmos valores foram utilizados para dopar o ZnS sendo, portanto, a terceiraetapa deste trabalho. O ZnS apresentou uma automontagem após o processo de dopagem. Esta automontagem não influenciou a energia obtida através de espectros de absorção na região UV-Vis. No entanto, observou-se que a concentração dos íons Mn2+aumenta no ZnS quando a presença do dopante foi analisada através da absorção atômica.Este aumento está em concordância com os espectros de emissão, os quais mostram um aumento do defeito proveniente de vacância de enxofre ou enxofre intersticial após o processo de dopagem indicando que os íons manganês, apesar da pequena concentração utilizada, estão presentes na estrutura do ZnS. A etapa final do trabalho consta de um novo arranjo supramolecular da estrutura cristalina do complexotiossemicarbazona de zinco [Zn(TPTSC)2], um potencial precursor molecular do tipo single-source para a obtenção de nanocristais semicondutores de ZnS em trabalhos futuros.

In this thesis, large organic molecules (DM15N, DM18N, Cu(dbm)2) were deposited. These molecules are cannot be deposited by thermal sublimation due the fact that they decompose at lower temperature than they sublime. The employed molecules to single molecular magnets, which can be potentially used as quantum bites (qubit). The new method of deposition atomic layer injection made by Bihur Crystal company was introduced and tested. The method uses liquid solution with molecules which is driven by argon gas through pulse valve to the sample placed in ultra-high vacuum chamber. During the deposition, droplets of solution are formed on the sample surface. The solvent can be removed by light annealing or by keeping the sample in the vacuum for couple of days. The molecules were investigated by x-ray photoelectron spectroscopy and by scanning electron microscopy to determine fragmentation of the molecules, to study topography of the resultant surface and homogeneity of the deposited layer. We found conditions at which the intact molecules are deposited on the sample surfaces and form molecular nano- and micro- crystals.