Patient-specific computational hemodynamics of intracranial aneurysms from 3D rotational angiography and CT angiography: an in vivo reproducibility study

Patient-specific simulations of the hemodynamics in intracranial aneurysms can be constructed by using image-based vascular models and CFD techniques. This work evaluates the impact of the choice of imaging technique on these simulations

Computational Approach to the Study of Thermal Spin Crossover Phenomena

The key parameters associated to the thermally induced spin crossover process have been calculated for a series of Fe(II) complexes with mono-, bi-, and tridentate ligands. Combination of density functional theory calculations for the geometries and for normal vibrational modes, and highly correlated wave function methods for the energies, allows us to accurately compute the entropy variation associated to the spin transition and the zero-point corrected energy difference between the low- and high-spin states. From these values, the transition temperature, T 1/2, is estimated for different compounds.

Optimizing Computational Frameworks to Study the Influence of the Protein Environment on the Individual Site Energies of Chromophores in Photosystem II of Photosynthesis

Photosynthesis is a process in which electromagnetic radiation is converted into chemical energy. Photosystems capture photons with chromophores and transfer their energy to reaction centers using chromophores as a medium. In the reaction center, the excitation energy is used to perform chemical reactions. Knowledge of chromophore site energies is crucial to the understanding of excitation energy transfer pathways in photosystems and the ability to compute the site energies in a fast and accurate manner is mandatory for investigating how protein dynamics ef-fect the site energies and ultimately energy pathways with time. In this work we developed two software frameworks designed to optimize the calculations of chro-mophore site energies within a protein environment. The first is for performing quantum mechanical energy optimizations on molecules and the second is for com-puting site energies of chromophores in a fast and accurate manner using the polar-izability embedding method. The two frameworks allow for the fast and accurate calculation of chromophore site energies within proteins, ultimately allowing for the effect of protein dynamics on energy pathways to be studied. We use these frame-works to compute the site energies of the eight chromophores in the reaction center of photosystem II (PSII) using a 1.9 Å resolution x-ray structure of photosystem II. We compare our results to conflicting experimental data obtained from both isolat-ed intact PSII core preparations and the minimal reaction center preparation of PSII, and find our work more supportive of the former.

A computational fluid dynamic study on the filtering mechanics in suspension feeding marine invertebrates

Les suspensivores ont la tâche importante de séparer les particules de l'eau. Bien qu'une grande gamme de morphologies existe pour les structures d'alimentation, elles sont pratiquement toutes constituées de rangées de cylindres qui interagissent avec leur environnement fluide. Le mécanisme de capture des particules utilisé dépend des contraintes morphologiques, des besoins énergétiques et des conditions d'écoulement. Comme nos objectifs étaient de comprendre ces relations, nous avons eu recours à des études de comparaison pour interpréter les tendances en nature et pour comprendre les conditions qui provoquent de nouveaux fonctionnements. Nous avons utilisé la dynamique des fluides numérique (computational fluid dynamics, CFD) pour créer des expériences contrôlées et pour simplifier les analyses. Notre première étude démontre que les coûts énergétiques associés au pompage dans les espaces petits sont élevés. De plus, le CFD suggère que les fentes branchiales des ptérobranches sont des structures rudimentaires, d'un ancêtre plus grande. Ce dernier point confirme l'hypothèse qu'un ver se nourrit par filtration tel que l'ancêtre des deuterostomes. Notre deuxième étude détermine la gamme du nombre de Reynolds number critique où la performance d'un filtre de balane change. Quand le Re est très bas, les différences morphologiques n'ont pas un grand effet sur le fonctionnement. Cependant, une pagaie devient une passoire lorsque le Re se trouve entre 1 et 3,5. Le CFD s’est dévoilé être un outil très utile qui a permis d’obtenir des détails sur les microfluides. Ces études montrent comment la morphologie et les dynamiques des fluides interagissent avec la mécanisme de capture ou de structures utilisées, ainsi que comment des petits changements de taille, de forme, ou de vitesse d'écoulement peuvent conduire à un nouveau fonctionnement.

Single and multiple addition to C60. A computational chemistry study

Des del seu descobriment, a la molècula C60 se li coneixen una varietat de derivats segons el tipus de funcionalització amb propietats fisicoquímiques específiques de gran interès científic. Una sel·lecció de derivats corresponents a addicions simple o múltiple al C60 s'ha considerat en aquest treball d'investigació. L'estudi a nivell de química computacional de diversos tipus d'addició al C60 s'han portat a terme per tal de poder donar resposta a aspectes que experimentalment no s'entenen o són poc clars. Els sistemes estudiats en referència a l'addició simple al C60 han estat en primer lloc els monoiminoful·lerens, C60NR, (de les dues vies proposades per la seva síntesi, anàlisis cinètic i termodinàmic han ajudat a explicar els mecanismes de formació i justificar l'addició a enllaços tipus [5,6]), i en segon lloc els metanoful·lerens i els hidroful·lerens substituits, C60CHR i C60HR, (raons geomètriques, electròniques, energètiques i magnètiques justifiquen el diferent caràcter àcid ente ambdós derivats tenint en compte una sèrie de substituents R amb diferent caràcter electrònic donor/acceptor). Els fluoroful·lerens, C60Fn, i els epoxid ful·lerens, C60On, (anàlisi sistemàtic dels seus patrons d'addició en base a poder justificar la força que els governa han aportat dades complementàries a les poques que existeixen experimentalment al respecte).

Study of the phenanthroline-Mn-imidazole bonding in Mn(I) triscarbonyl complex: A X-ray and DFT computational analysis

355 nm light irradiation of fac-[Mn(CO)(3)(phen)(imH)](+) (fac-1) produces the mer-1 isomer and a long lived radical which can be efficiently trapped by electron acceptor molecules. EPR experiments shows that when excited, the manganese(I) complex can be readily oxidized by one-electron process to produce Mn(II) and phen(.-). In the present study, DFT calculations have been used to investigated the photochemical isomerization of the parent Mn(I) complex and to characterize the electronic structures of the long lived radical. The theoretical calculations have been performed on both the fac-1 and mer-1 species as well as on their one electron oxidized species fac-1+ and mer-1+ for the lowest spin configurations (S = 1/2) and fac-6 and mer-6 (S = 5/2) for the highest one to characterize these complexes. In particular, we used a charge decomposition analysis (CDA) and a natural bonding orbital (NBO) to have a better understanding of the chemical bonding in terms of the nature of electronic interactions. The observed variations in geometry and bond energies with an increasing oxidation state in the central metal ion are interpreted in terms of changes in the nature of metal-ligand bonding interactions. The X-ray structure of fac-1 is also described. (C) 2011 Elsevier B.V. All rights reserved.

A joint computational and experimental study of a novel dioxomolybdenum(VI) complex bearing chiral N,N-dimethyllactamide ligand

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Gas-phase reactivity of 2-hydroxy-1,4-naphthoquinones: a computational and mass spectrometry study of lapachol congeners

In order to understand the influence of alkyl side chains on the gas-phase reactivity of 1,4-naphthoquinone derivatives, some 2-hydroxy-1,4-naphthoquinone derivatives have been prepared and studied by electrospray ionization tandem mass spectrometry in combination with computational quantum chemistry calculations. Protonation and deprotonation sites were suggested on the basis of gas-phase basicity, proton affinity, gas-phase acidity (?Gacid), atomic charges and frontier orbital analyses. The nature of the intramolecular interaction as well as of the hydrogen bond in the systems was investigated by the atoms-in-molecules theory and the natural bond orbital analysis. The results were compared with data published for lapachol (2-hydroxy-3-(3-methyl-2-butenyl)-1,4-naphthoquinone). For the protonated molecules, water elimination was verified to occur at lower proportion when compared with side chain elimination, as evidenced in earlier studies on lapachol. The side chain at position C(3) was found to play important roles in the fragmentation mechanisms of these compounds. Copyright (c) 2012 John Wiley & Sons, Ltd.

"Experimental and computational approaches to historical masonry structures: A study in the direction of filling the gap"

The assessment of historical structures is a significant need for the next generations, as historical monuments represent the community’s identity and have an important cultural value to society. Most of historical structures built by using masonry which is one of the oldest and most common construction materials used in the building sector since the ancient time. Also it is considered a complex material, as it is a composition of brick units and mortar, which affects the structural performance of the building by having different mechanical behaviour with respect to different geometry and qualities given by the components.

Computational biomechanics to simulate the femoropopliteal intersection during knee flexion: a preliminary study

To assess if finite element (FE) models can be used to predict deformation of the femoropopliteal segment during knee flexion.

Integration of computational models and experimental characterization to study internal frost damage in cementitious materials

The objective of this doctoral research is to investigate the internal frost damage due to crystallization pore pressure in porous cement-based materials by developing computational and experimental characterization tools. As an essential component of the U.S. infrastructure system, the durability of concrete has significant impact on maintenance costs. In cold climates, freeze-thaw damage is a major issue affecting the durability of concrete. The deleterious effects of the freeze-thaw cycle depend on the microscale characteristics of concrete such as the pore sizes and the pore distribution, as well as the environmental conditions. Recent theories attribute internal frost damage of concrete is caused by crystallization pore pressure in the cold environment. The pore structures have significant impact on freeze-thaw durability of cement/concrete samples. The scanning electron microscope (SEM) and transmission X-ray microscopy (TXM) techniques were applied to characterize freeze-thaw damage within pore structure. In the microscale pore system, the crystallization pressures at sub-cooling temperatures were calculated using interface energy balance with thermodynamic analysis. The multi-phase Extended Finite Element Modeling (XFEM) and bilinear Cohesive Zone Modeling (CZM) were developed to simulate the internal frost damage of heterogeneous cement-based material samples. The fracture simulation with these two techniques were validated by comparing the predicted fracture behavior with the captured damage from compact tension (CT) and single-edge notched beam (SEB) bending tests. The study applied the developed computational tools to simulate the internal frost damage caused by ice crystallization with the two dimensional (2-D) SEM and three dimensional (3-D) reconstructed SEM and TXM digital samples. The pore pressure calculated from thermodynamic analysis was input for model simulation. The 2-D and 3-D bilinear CZM predicted the crack initiation and propagation within cement paste microstructure. The favorably predicted crack paths in concrete/cement samples indicate the developed bilinear CZM techniques have the ability to capture crack nucleation and propagation in cement-based material samples with multiphase and associated interface. By comparing the computational prediction with the actual damaged samples, it also indicates that the ice crystallization pressure is the main mechanism for the internal frost damage in cementitious materials.

Flow disturbances in stent-related coronary evaginations: a computational fluid-dynamic simulation study

Aims: Angiographic ectasias and aneurysms in stented segments have been associated with late stent thrombosis. Using optical coherence tomography (OCT), some stented segments show coronary evaginations reminiscent of ectasias. The purpose of this study was to explore, using computational fluid-dynamic (CFD) simulations, whether OCT-detected coronary evaginations can induce local changes in blood flow. Methods and results: OCT-detected evaginations are defined as outward bulges in the luminal vessel contour between struts, with the depth of the bulge exceeding the actual strut thickness. Evaginations can be characterised cross ectionally by depth and along the stented segment by total length. Assuming an ellipsoid shape, we modelled 3-D evaginations with different sizes by varying the depth from 0.2-1.0 mm, and the length from 1-9 mm. For the flow simulation we used average flow velocity data from non-diseased coronary arteries. The change in flow with varying evagination sizes was assessed using a particle tracing test where the particle transit time within the segment with evagination was compared with that of a control vessel. The presence of the evagination caused a delayed particle transit time which increased with the evagination size. The change in flow consisted locally of recirculation within the evagination, as well as flow deceleration due to a larger lumen - seen as a deflection of flow towards the evagination. Conclusions: CFD simulation of 3-D evaginations and blood flow suggests that evaginations affect flow locally, with a flow disturbance that increases with increasing evagination size.

A longitudinal study of Type-B aortic dissection and endovascular repair scenarios: computational analyses

Conservative medical treatment is commonly first recommended for patients with uncomplicated Type-B aortic dissection (AD). However, if dissection-related complications occur, endovascular repair or open surgery is performed. Here we establish computational models of AD based on radiological three-dimensional images of a patient at initial presentation and after 4-years of best medical treatment (BMT). Computational fluid dynamics analyses are performed to quantitatively investigate the hemodynamic features of AD. Entry and re-entries (functioning as entries and outlets) are identified in the initial and follow-up models, and obvious variations of the inter-luminal flow exchange are revealed. Computational studies indicate that the reduction of blood pressure in BMT patients lowers pressure and wall shear stress in the thoracic aorta in general, and flattens the pressure distribution on the outer wall of the dissection, potentially reducing the progressive enlargement of the false lumen. Finally, scenario studies of endovascular aortic repair are conducted. The results indicate that, for patients with multiple tears, stent-grafts occluding all re-entries would be required to effectively reduce inter-luminal blood communication and thus induce thrombosis in the false lumen. This implicates that computational flow analyses may identify entries and relevant re-entries between true and false lumen and potentially assist in stent-graft planning.