Estudo da estrutura e da solvatação do HNP-3, um antibiótico natural, por dinâmica molecular

The structure and hydration of the HNP-3 have been derived from molecular dynamics data using root mean square deviation, radial and energy distributions. Three antiparallel beta sheets were found to be preserved. 15 intramolecular hydrogen bonds were identified together with 36 hydrogen bonds on the backbone and 35 on the side chain atoms. From the point of view of the hydration dynamics, the analysis shows a high solvent accessibility of the monomer and attractive interactions with water molecules.

Estrutura e propriedades de elipticinas

The ellipticines constitute a broad class of molecules with antitumor activity. In the present work we analyzed the structure and properties of a series of ellipticine derivatives in the gas phase and in solution using quantum mechanical and Monte Carlo methods. The results showed a good correlation between the solvation energies in water obtained with the continuum model and the Monte Carlo simulation. Molecular descriptors were considered in the development of QSAR models using the DNA association constant (log Kapp) as biological data. The results showed that the DNA binding is dominated by electronic parameters, with small contributions from the molecular volume and area.

Real-Time Simulation of Mobile and Industrial Machines Using the Multibody Simulation Approach

This thesis introduces a real-time simulation environment based on the multibody simulation approach. The environment consists of components that are used in conventional product development, including computer aided drawing, visualization, dynamic simulation and finite element software architecture, data transfer and haptics. These components are combined to perform as a coupled system on one platform. The environment is used to simulate mobile and industrial machines at different stages of a product life time. Consequently, the demands of the simulated scenarios vary. In this thesis, a real-time simulation environment based on the multibody approach is used to study a reel mechanism of a paper machine and a gantry crane. These case systems are used to demonstrate the usability of the real-time simulation environment for fault detection purposes and in the context of a training simulator. In order to describe the dynamical performance of a mobile or industrial machine, the nonlinear equations of motion must be defined. In this thesis, the dynamical behaviour of machines is modelled using the multibody simulation approach. A multibody system may consist of rigid and flexible bodies which are joined using kinematic joint constraints while force components are used to describe the actuators. The strength of multibody dynamics relies upon its ability to describe nonlinearities arising from wearing of the components, friction, large rotations or contact forces in a systematic manner. For this reason, the interfaces between subsystems such as mechanics, hydraulics and control systems of the mechatronic machine can be defined and analyzed in a straightforward manner.

Estrutura e propriedades da difenil-4-amina sulfonato de sódio: um dopante de filmes condutores

This work contains the theoretical simulation of the conformation of diphenyl-4-amine sodium sulphonate (DASNa) and correlates its geometry with conductivity, showing that the conductivity increases as the molecule becomes more planar. The solvent effect was also evaluated, using water and dimethylsulfoxide. Some properties, such as bond distance, vibration al frequency and effective charge were calculated. The utilization of diphenyl-4-amine sodium sulphonate (DASNa) as dopant of aniline was investigated in view of the HOMO-LUMO energy gap.

Improved understanding of drought controls on seasonal variation in Mediterranean forest canopy CO2 and water fluxes through combined in situ measurements and ecosystem modelling

Water stress is a defining characteristic of Mediterranean ecosystems, and is likely to become more severe in the coming decades. Simulation models are key tools for making predictions, but our current understanding of how soil moisture controls ecosystem functioning is not sufficient to adequately constrain parameterisations. Canopy-scale flux data from four forest ecosystems with Mediterranean-type climates were used in order to analyse the physiological controls on carbon and water flues through the year. Significant non-stomatal limitations on photosynthesis were detected, along with lesser changes in the conductance-assimilation relationship. New model parameterisations were derived and implemented in two contrasting modelling approaches. The effectiveness of two models, one a dynamic global vegetation model ('ORCHIDEE'), and the other a forest growth model particularly developed for Mediterranean simulations ('GOTILWA+'), was assessed and modelled canopy responses to seasonal changes in soil moisture were analysed in comparison with in situ flux measurements. In contrast to commonly held assumptions, we find that changing the ratio of conductance to assimilation under natural, seasonally-developing, soil moisture stress is not sufficient to reproduce forest canopy CO2 and water fluxes. However, accurate predictions of both CO2 and water fluxes under all soil moisture levels encountered in the field are obtained if photosynthetic capacity is assumed to vary with soil moisture. This new parameterisation has important consequences for simulated responses of carbon and water fluxes to seasonal soil moisture stress, and should greatly improve our ability to anticipate future impacts of climate changes on the functioning of ecosystems in Mediterranean-type climates.

Water circulations for effective bleaching of high-brightness mechanical pulps

The amount of water available is usually restricted, which leads to a situation where a complete understanding of the process, including water circulations and the influence of water components, is essential. The main aim of this thesis was to clarify the possibilities for the efficient use of residual peroxide by means of water circulation rearrangements. Rearranging water circulations and the reduction of water usage may cause new problems, such as metal induced peroxide decomposition that needs to be addressed. This thesis introduces theoretical methods of water circulations to combine two variables; effective utilization of residual peroxide and avoiding manganese in the alkaline peroxide bleaching stage. Results are mainly based on laboratory and mill site experiments concerning the utilization of residual peroxide. A simulation model (BALAS) was used to evaluate the manganese contents and residual peroxide doses. It was shown that with optimum recirculation of residual peroxide the brightness can be improved or chemical costs can be decreased. From the scientific perspective, it was also very important to discover that recycled peroxide was more effective pre-bleaching agent compared to fresh peroxide. This can be due to the organic acids i.e. per acetic acid in wash press filtrate that have been formed in alkaline bleaching stage. Even short retention time was adequate and the activation of residual peroxide using sodium hydroxide was not necessary. There are several possibilities for using residual peroxide in practice regarding bleaching. A typical modern mechanical pulping process line consist of defibering, screening, a disc filter, a bleach press, high consistency (HC) peroxide bleaching and a wash press. Furthermore there usually is not a particular medium consistency (MC) pre-bleaching stage that includes additional thickening equipment. The most advisable way to utilize residual peroxide in this kind of process is to recycle the wash press filtrate to the dilution of disc filter pulp (low MC pre-bleaching stage). An arrangement such as this would be beneficial in terms of the reduced convection of manganese to the alkaline bleaching stage. Manganese originates from wood material and will be removed to the water phase already in the early stages of the process. Recycling residual peroxide prior to the disc filter is not recommended because of low consistencies. Regarding water circulations, the novel point of view is that, it would be beneficial to divide water circulations into two sections and the critical location for the division is the disc filter. Both of these two sections have their own priority. Section one before the disc filter: manganese removal. Section two after the disc filter: brightening of pulp. This division can be carried out if the disc filter pulp is diluted only by wash press filtrate before the MC storage tower. The situation is even better if there is an additional press after the disc filter, which will improve the consistency of the pulp. This has a significant effect on the peroxide concentration in the MC pre-bleaching stage. In terms of manganese content, it is essential to avoid the use of disc filter filtrate in the bleach press and wash press showers. An additional cut-off press would also be beneficial for manganese removal. As a combination of higher initial brightness and lower manganese content, the typical brightness increase varies between approximately 0.5 and 1% ISO units after the alkaline peroxide bleaching stage. This improvement does not seem to be remarkable, but as it is generally known, the final brightness unit is the most expensive and difficult to achieve. The estimation of cost savings is not unambiguous. For example in GW/TMP mill case 0.6% ISO units higher final brightness gave 10% savings in the costs of bleaching chemicals. With an hypothetical 200 000 ton annual production, this means that the mill could save in the costs of bleaching chemicals more than 400 000 euros per year. In general, it can be said that there were no differences between the behavior of different types of processes (GW, PGW, TMP and BCTMP). The enhancement of recycling gave a similar response in all cases. However, we have to remember that the utilization of residual peroxide in older mills depends a great deal on the process equipment, the amount of water available and existing pipeline connections. In summary, it can be said that processes are individual and the same solutions cannot be applied to all cases.

An Engineering Solution for using Coarse Meshes in the Simulation of Delamination with Cohesive Zone Models

This paper presents a methodology to determine the parameters used in the simulation of delamination in composite materials using decohesion finite elements. A closed-form expression is developed to define the stiffness of the cohesive layer. A novel procedure that allows the use of coarser meshes of decohesion elements in large-scale computations is proposed. The procedure ensures that the energy dissipated by the fracture process is correctly computed. It is shown that coarse-meshed models defined using the approach proposed here yield the same results as the models with finer meshes normally used in the simulation of fracture processes

Simulation of Delamination Propagation in Composites Under High-Cycle Fatigue by Means of Cohesive-Zone Models

A damage model for the simulation of delamination propagation under high-cycle fatigue loading is proposed. The basis for the formulation is a cohesive law that links fracture and damage mechanics to establish the evolution of the damage variable in terms of the crack growth rate dA/dN. The damage state is obtained as a function of the loading conditions as well as the experimentally-determined coefficients of the Paris Law crack propagation rates for the material. It is shown that by using the constitutive fatigue damage model in a structural analysis, experimental results can be reproduced without the need of additional model-specific curve-fitting parameters

An Interface Damage Model for the Simulation of Delamination Under Variable-Mode Ratio in Composite Materials

A thermodynamically consistent damage model for the simulation of progressive delamination under variable mode ratio is presented. The model is formulated in the context of the Damage Mechanics. The constitutive equation that results from the definition of the free energy as a function of a damage variable is used to model the initiation and propagation of delamination. A new delamination initiation criterion is developed to assure that the formulation can account for changes in the loading mode in a thermodynamically consistent way. The formulation proposed accounts for crack closure effets avoiding interfacial penetration of two adjacent layers aftercomplete decohesion. The model is implemented in a finite element formulation. The numerical predictions given by the model are compared with experimental results

Aaltovoimalaitteen toimintaperiaatteen analysointi

Diplomityö tehtiin Wello Oy:n toimeksiannosta. Wello Oy on vesi- ja tuulivoimaratkaisuihin keskittynyt yritys, joka kehittää aaltovoimalaitekonseptia. Työssä selvitettiin aaltovoimaan liittyviä ilmiöitä ja aaltovoimalaitteen mekaanista konseptia ja tehtiin arvio niiden tehokkuudesta. Työssä käytettiin kaupallisia simulointityökaluja kuten monikappaledynamiikan simulointiohjelmaa MSC.ADAMS R3:a ja yleistä matematiikka ohjelmaa Matlab Simulink:ia. Simulointimallia käytettiin arvioimaan laitteen yleistä käyttäytymistä. Lisäksi laitteen analyyttisiä malleja käytettiin laitteen toimintaperiaatteen selvitykseen. Simulointia käytettiin kelluvan laitteen mekanismin tutkimukseen. Tuloksiin pohjautuen laitteelle määriteltiin teoreettiset maksimiteho rajat ja rajoitteet, jotka vaikuttavat laitteen tehokkuuteen.

Bases moleculares da ação anti-inflamatória dos ácidos oleanólico e ursólico sobre as isoformas da ciclo-oxigenase por docking e dinâmica molecular

The triterpenoids oleanolic (OA) and ursolic (UA) acids show non-selective antiinflamatory activity in vitro for cyclooxygenase (COX) isoforms. 3D conformations of OA and UA, with three possible orientations (1, 1' and 2) in the active site of isoforms COX, obtained by docking, were submitted to molecular dynamics. The results show that orientation 2 of the OA in COX-2 is more favorable because orientation 1 moved away from the active site. The carboxylate group of OA interact by hydrogen bonds with Ser353 and with Phe357 and Leu359, mediated by water, while hydroxyl in C-3 interact by hydrogen bond, mediated by water, with Tyr385.

Investigating the spontaneous formation of SDS micelle in aqueous solution using a coarse-grained force field

A 1µs Molecular Dynamic simulation was performed with a realistic model system of Sodium Dodecyl Sulfate (SDS) micelles in aqueous solution, comprising of 360 DS-, 360 Na+ and 90000 water particles. After 300 ns three different micellar shapes and sizes 41, 68 and 95 monomers, were observed. The process led to stabilization in the total number of SDS clusters and an increase in the micellar radius to 2.23 nm, in agreement with experimental results. An important conclusion, is be aware that simulations employed in one aggregate, should be considered as a constraint. Size and shape distribution must be analyzed.

EFEITO DA ESTRUTURA MOLECULAR DE LIGANTES DE SUPERFÍCIE EM PONTOS QUÂNTICOS DE CdTe DISPERSOS EM ÁGUA

Water-soluble CdTe quantum dots are synthesized to investigate how short-chain surface ligands bearing -SH, -COOH, and -NH2 groups interact with CdTe during nucleation/growth processes. Their optical properties and colloidal stability after the ligand exchange are also investigated. We then characterize the resulting CdTe by fluorescence, UV–Vis absorption, and infrared spectroscopies. The stability of the colloidal dispersions was determined by their Zeta potentials. The results show that in the synthesis of water-soluble CdTe, surface ligands with at least two functional groups are required and the hard/soft character of them is an important factor in the stability of CdTe.

TRIHALOMETANOS EM ÁGUA POTÁVEL E RISCOS DE CÂNCER: SIMULAÇÃO USANDO POTENCIAL DE INTERAÇÃO E TRANSFORMAÇÕES DE BÄCKLUND

We briefly investigated the well-known correlation of trihalomethanes, present in fresh water, with cancer hazard in humans. A transient alternative method of chemical simulation using Bäcklund Transformations and Quantum Mechanics is presented. Finally, the method was applied to simulate the interaction between Trichloridemethane and Alanine - as well as its amino and carboxyl groups.

USO DA RMN DE BAIXA RESOLUÇÃO NA AVALIAÇÃO DA DINÂMICA MOLECULAR DO Origanum vulgare

In this work, proton NMR relaxometry was used to measure the behavior of spin-lattice relaxation time with T1H as the time constant, and also of spin-spin relaxation time with the time constant T2H. These relaxometry parameters were determined to better understand the changes in the main structures present in commercial and in nature forms of origanum. The T1H relaxation data showed that the structures which had higher molecular mass were more sensitive to degradation with increased temperature treatment. According to the values of the T2H parameter, up to 150 degrees no significant change in the mobility and organization of water was observed. These data infer that the ideal cooking temperature and tea preparation mode for this herb should be around 100 degrees for the sample not to lose its characteristics. Also, it is not advisable to cook this herb at higher than 150 degrees but better to consume it at room temperature, especially give commercial herb has already been dehydrated.