This paper considers the statistical mechanics occupation of the edge of a single helix of DNA by simple polymers. Using Fisher's exact closed form solution for dimers on a two-dimensional lattice, a one-dimensional lattice is created mathematically that is occupied by dimers, monomers, and holes. The free energy, entropy, average occupation, and total charge on the lattice are found through the usual statistical methods. The results demonstrate the charge inversion required for a DNA helix to undergo DNA condensation.

The fibrinogen degradation product D-dimer is released in plasma during fibrinolysis. D-dimer analysis is mainly ordered for the exclusion of venous thromboembolism (VTE) in combination with a pre-test probability (PTP) score. D-dimer below 0,5 mg/L fibrinogen equivalent units (FEU) and a low PTP rules out VTE. D-dimer analysis contributes to the reduction of invasive and expensive imaging analyses, such as ultrasound and computed tomography. The Blekinge region primary care used a qualitative D-dimer point of care test (POCT) whose performance the clinical chemistry of Blekinge hospital had no insight into. The aim of the study was to investigate whether the qualitative D-dimer POCT was an adequate complement to the quantitative method used in the hospital laboratory. Fifty patients, whose blood samples arrived the laboratory in tubes with sodium citrate- and ethylenediaminetetraacetic acid (EDTA) additives, were chosen for the study. Citrate plasma was analyzed with the D-dimer laboratory method. Plasma and whole blood were analyzed with the D-dimer POCT. Quantitative results were converted to qualitative based on the cutoff value 0,5 mg/L FEU. POCT performance was computed and compared with the manufacturer’s specified values. A potential difference between the methods was evaluated with a Chi-squared test. A survey was performed where open care units answered questions regarding D-dimer POCT. The POCT performance was slightly lower than the manufacturer’s specifications. No statistically significant difference was seen between the methods. However, there were several sources of error with the latter. Some open care units mentioned weak lines in the reading area due to blood interference. / Vid fibrinolys av blodkoagel frisätts fibrinnedbrytningsprodukten D-dimer. D-dimeranalyser utförs främst för uteslutning av venös tromboembolism (VTE) i kombination med ett poängsystem för preanalytisk sannolikhet (PTP) för VTE. D-dimerhalter under 0,5 mg/L fibrinogenekvivalenta enheter (FEU) och en låg PTP utesluter med stor säkerhet VTE. Använd på rätt sätt bidrar D-dimeranalysen till att minimera onödiga invasiva och dyra undersökningar som ultraljud och datortomografi. I region Blekinge används en kvalitativ, patientnära analysmetod (PNA) för D-dimer vars prestanda Blekingesjukhusets laboratorium för klinisk kemi inte har någon insyn i. Studiens syfte var att undersöka om den kvalitativa PNA-metoden för D-dimer utgjorde ett lämpligt komplement till den kvantitativa metod som utfördes på klinisk kemi. Femtio patienter vars blodprov anlände laboratoriet i provrör med tillsats av natriumcitrat respektive etylendiamintetraättiksyra (EDTA) blev utvalda att delta i studien. D-dimer analyserades i citratplasma med laboratoriets analysmetod varefter plasma och tillhörande EDTA-blod analyserades med PNA-metoden. Kvantitativa resultat konverterades till kvalitativa efter beslutsvärdet 0,5 mg/L FEU. PNA-prestandan beräknades och jämfördes med tillverkarens angivna motsvarigheter. Med ett chi-squaretest undersöktes en eventuell signifikant skillnad mellan metodresultaten. En undersökning utfördes där regionens öppenvårdsenheter svarade på diverse frågor kring PNA-metoden. PNA-metodens beräknade prestanda var något lägre än tillverkarens. Ingen statistiskt signifikant skillnad förekom mellan laboratoriets metod och PNA-metoden, däremot fanns det flera potentiella felkällor hos den senare. Några öppenvårdsenheter vittnade om svåravlästa avläsningsområden på grund av blodinterferens.

Resolvemos o modelo de d´meros em duas redes planas diferentes, a rede 4-8 e a rede hexagonal (favo de mel). Na rede 4-8 ocorre uma transição do tipo Ising (bidimensional); na rede hexagonal há uma transição conhecida como 3/2. Após a definição do modelo mostramos que o cálculo da função de partição pode ser formulado em termos do traço de uma matriz de transferência escrita numa representação de matrizes de Pauli. Usando a transformação de Jordan-Wigner, os operadores de Pauli são transformados em operadores de criação e aniquilação de férmions, e a matriz de transferência pode ser diagonalizada pela redução a um problema de férmions livres. Comparamos as soluções do modelo de dímeros na rede 4-8 e do modelo de Ising bidimensional; em particular, comparamos o comportamento do calor específico e analisamos o espectro da matriz de transferência. Verificamos que as nossas soluções concordam com resultados obtidos pelas técnicas combinatórias. Utilizamos a formulação da matriz de transferência para construir uma versão de tempo contínuo dos modelos de dímeros nas redes quadrada, 4-8 e hexagonal. Ao contrário do modelo de Ising, no caso dos dímeros essa aproximação de tempo contínuo altera a natureza do comportamento crítico. / We solve the dimer model on two different planar lattices, the 4-8 lattice and the honeycomb lattice. In the dimer model on the 4-8 lattice there is a phase transition of the (two-dimensional) Ising type; on the honeycomb lattice there is a phase transition known as 3/2. After defining the model we show that the calculation of the partition function can be formulated as the trace of a transfer matrix that is written in terms of Pauli matrices. Using the Jordan-Wigner transformation, the Pauli matrices give rise to fermion creation and annihilation operators, and the problem is reduced to the diagonalization of a system of free fermions. We compare the solutions of the dimer model on the 4-8 lattice and of the two-dimensional Ising model; in particular, we compare the behavior of the specific heat and we analyze the spectrum of the transfer matrix. These solutions agree with well-known results from combinatorial techniques. We then use the transfer matrix approach to obtain a continuum time formulation for the dimer models on the square, 4-8 an d honeycomb lattices. In contrast to the Ising case, for the dimer models this approximation changes the nature of critical behavior.

We have used ab initio computational simulation techniques to investigate both intra- and intermolecular interactions in a novel family of ionic organophosphonate molecular crystals. We have examined the influence of various numerical approximations on the computed geometry and binding energies of a selection of well-characterised hydrogen bonded systems. It was found that numerical basis sets provided the efficiency required to study the large hydrogen bonded dimer anions present in the organophosphonate system, while also producing accurate geometries and binding energies. We then calculated the relaxed structures and binding energies of phenylphosphonic acid dimer in the two arrangements in which it is present in the bulk crystal. The computed geometries were in excellent agreement with the experimental structures and the binding energies were consistent with those found for other ionic hydrogen bonded systems. Electron density maps were used to gain insight into the nature of the hydrogen bonding interaction between phenylphosphonic acid dimers. We also examined the effect of aromatic ring substituents on the geometry and energetics of the hydrogen bonding interaction. The nitro-substituted dimer was predicted to have a stronger binding energy than its unsubstituted parent while the methyl-substituted dimer was predicted to have a similar binding energy to its unsubstituted parent. An analysis of crystal field effects showed that the structure of the phenylphosphonic acid dimers in the organophosphonates is a complex product of competing intra- and intermolecular forces and crystal field effects. Cooperative effects in the organophosphonate system were also investigated and it was found that the interactions were mostly one-body (local) in nature. We have examined the intramolecular charge-transfer interaction between copper-halogen cations in the organophosphonate materials. The origin of geometric differences between the Cu(I) starting material and Cu(II) product cations was attributed to the electronic configuration of the Cu ion, not crystal field effects. To gain further insight into the difference in electronic structure between the starting material and product, we attempted to simulate the step-by-step dissociation of the [CuI]+ system. Although this investigation was not successful, we were able to expose some of the pitfalls of simulating dissociating odd-electron systems. We also analysed and compared the charge-transfer interaction in the chloro-, bromo- and iodo-forms of the organophosphonate family. The charge-transfer interaction was predicted to increase on going from the chloro- to the iodo-form, consistent with solid-state UV-visible data. Finally, we used the highly accurate Quantum Monte Carlo (QMC) method to investigate the hydrogen bonding interaction in water dimer and to calculate the dissociation energy. The accuracy of the experimental estimate for the dissociation energy has recently been questioned and an alternative value has been put forward. Our results lend support to the validity of the alternative value and are also in excellent agreement with those from other high-level calculations. Our results also indicate that QMC techniques are a promising alternative to traditional wavefunction techniques in situations where both high accuracy and efficiency are important.

Nous étudions, dans la première partie de notre thèse, les polysimplexes d’un espace euclidien de dimension quelconque, c’est-à-dire les objets consistant en une juxtaposition de simplexes réguliers (de tétraèdres si la dimension est 3) accolés le long de leurs faces. Nous étudions principalement le groupe des symétries de ces polysimplexes. Nous présentons une façon de représenter un polysimplexe à l’aide d’un diagramme. Ceci fournit une classification complète des polysimplexes à similitude près. De plus, le groupe des symétries se déduit du groupe des automorphismes du diagramme. Il découle en particulier de notre étude qu’en dimension supérieure à 2, une telle structure ne possède jamais deux faces parallèles et ne contient jamais de circuit fermé de simplexes. Dans la seconde partie de notre thèse, nous abordons un problème classique de combinatoire : l’énumération des pavages d’un rectangle mxn à l’aide de dominos. Klarner et Pollack ont montré qu’en fixant m la suite obtenue vérifie une relation de récurrence linéaire à coefficients constants. Nous établissons une nouvelle méthode nous permettant d’obtenir la fonction génératrice correspondante et la calculons pour m <= 16, alors qu’elle n’était connue que pour m <= 10.

Small molecule mediated chemical intervention of biological processes using nucleic acid targets has proven extremely successful and is continually providing exciting new avenues for the development of anti-cancer agents and molecular probes. Among the alternative DNA confrormations, G-quadruplexes has certainly garnered much recognition due to increase in evidences supporting their involvement in diverse biological process. The grooves of the quadruplexes offer an alternate recognition site for ligand interactions with potentially higher selectivity than the traditional terminal stacking sites. DB832, a bifuryl-phenyl diamidine, was recently reported to selectively recognize human telomeric G-quadruplex, as a stacked species, with significant selectivity over duplex sequences. A series of biophysical studies were conducted to test the groove-binding mode of DB832, along with the selectivity for diverse quadruplex forming sequences. To gain better understanding of quadruplex groove-recognition by DB832, a series of structurally similar heterocyclic diamidines were also evaluated. The unique binding mode of DB832 may allow it to serve as a paradigm for the design of new class of highly selective quadruplex groove-binding molecules. Beyond the alternative secondary structures, it is also becoming increasingly apparent that the structure and dynamics of the canonical Watson–Crick DNA double helix play pivotal roles in diverse biological functions. DB1878, a phenyl-furan-indole diamidine, was shown to recognize a mixed GC/AT motif as a stacked antiparallel dimer, and a detailed structural analysis is reported here. Interestingly, the DNA recognition is completely different from the reported molecules in literature, and represents an entirely new motif for DNA minor groove recognition.

The Morse/Long Range (MLR) potential has become one of the most reliable and highly used potential energy functions for diatomic molecules. It includes the theoretical long range behaviour that diatomic molecules are known to exhibit as they approach the dissociation limit. Heavy alkali metals with adjacent electronic states often exhibit strong coupling between the spin and orbital angular momentum. The ground state X¹Σg⁺ and the lowest lying triplet state aᶟΣᵤ⁺ of Cs₂ exhibit such coupling effects and as a result, modeling the highest vibrational states of these states is a non-trivial problem. Utilizing scattering length values obtained from published analysis of 60 Feshbach resonances, the correct form of the potential energy function was determined. Moreover, the scattering length values were used to determine the correct leading dispersion coefficient that describes the true form of the long-range potential energy functions. All previous attempts to determine global potential energy functions for these states have considered only the optical spectroscopic data. This is the first ever effort attempting to use scattering lengths determined from cold atom collision experiments in a combined analysis with conventional spectroscopic data.

No description available.

The strong electromagnetic field that is induced at the surface of a plasmonic nanoparticle can be utilized for many important applications, including spectroscopic enhancement and electromagnetic waveguides. The focus of this thesis is to study some of the properties of induced plasmonic fields around metal nanoparticles. Current methodologies for fabricating nanoparticles are discussed, including lithography and colloidal synthesis. This dissertation includes studies on plasmonic driven nanoparticle motion of surface supported gold nanoprisms from a substrate into solution via a femtosecond pulse. The mechanism of particle motion is discussed and the stability of the unprotected nanoprisms in solution is studied. Fundamental plasmonic near-field coupling between two plasmonic nanoparticles is also examined. Experimental results using electron beam lithography fabricated samples are used to explicitly describe the plasmonic coupling between dimers as a function of the nanoparticle size, shape, and orientation. These variables are systematically studied and the dependence is compared to mathematically derived functional dependencies in order to model and predict the effects of plasmonic coupling. As an extension, the coupling between plasmonic nanoparticles is shown in a common application, surface enhanced Raman scattering. The final chapter is devoted to an investigation of the nature of nanocatalysis, homogeneous and heterogeneous, for several reactions using metal nanoparticles.

No description available.