STUDY ON CYCLODEXTRIN AND ITS INCLUSION COMPLEXES - MOLECULAR MECHANICAL CALCULATION

We studied several inclusion complexes of beta-CD by means of molecular mechanical calculation. The inclusion process and the driving force were discussed, and the conclusion on stability agrees with the results of electrochemical experiments.

Thermo-mechanical modelling of power electronics module structures

Power electronic modules distinguish themselves from other modules by their high power operation. These modules are used extensively in high power application markets such as aerospace, automotive, industrial and traction and drives. This paper discusses typical packaging technologies for power electronics modules. It also discusses the latest results from a UK research project investigating the physics-of-failure approach to reliability analysis and predictions for power modules. An integrated design enviroment for incorporating of affects of uncertainty into the design environment was outlined.

Thermal-mechanical modelling of power electronic module packaging

In this paper the reliability of the isolation substrate and chip mountdown solder interconnect of power modules under thermal-mechanical loading has been analysed using a numerical modelling approach. The damage indicators such as the peel stress and the accumulated plastic work density in solder interconnect are calculated for a range of geometrical design parameters, and the effects of these parameters on the reliability are studied by using a combination of the finite element analysis (FEA) method and optimisation techniques. The sensitivities of the reliability of the isolation substrate and solder interconnect to the changes of the design parameters are obtained and optimal designs are studied using response surface approximation and gradient optimization method

A tellurium-based cathepsin B inhibitor: Molecular structure, modelling, molecular docking and biological evaluation

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

A tellurium-based cathepsin B inhibitor: Molecular structure, modelling, molecular docking and biological evaluation

The crystallographically determined structure of biologically active 4,4-dichloro-1,3-diphenyl-4-telluraoct-2-en-1-one, 3, shows the coordination geometry for Te to be distorted psi-pentagonal bipyramidal based on a C2OCl3(lone pair) donor set. Notable is the presence of an intramolecular axial Te center dot center dot center dot O (carbonyl) interaction, a design element included to reduce hydrolysis. Raman and molecular modelling studies indicate the persistence of the Te center dot center dot center dot O(carbonyl) interaction in the solution (CHCl3) and gasphases, respectively. Docking studies of 3' (i.e. original 3 less one chloride) with Cathepsin B reveals a change in the configuration about the vinyl C = C bond. i.e. to E from Z (crystal structure). This isomerism allows the optimisation of interactions in the complex which features a covalent Te-SGCys29 bond. Crucially, the E configuration observed for 3' allows for the formation of a hypervalent Te center dot center dot center dot O interaction as well as an O center dot center dot center dot H-O hydrogen bond with the Gly27 and Glu122 residues, respectively. Additional stabilisation is afforded by a combination of interactions spanning the S1, S2, S1' and S2' sub-sites of Cathepsin B. The greater experimental inhibitory activity of 3 compared with analogues is rationalised by the additional interactions formed between 3' and the His110 and His111 residues in the occluding loop, which serve to hinder the entrance to the active site. (C) 2012 Elsevier B.V. All rights reserved.

Determining day length and temperature regulation of flowering: a molecular and modelling approach

Thesis (Ph.D.)--University of Washington, 2016-08

A three dimensional finite volume approach to the thermo-mechanical modelling of the shape casting of metals

This paper presents a three dimensional, thermos-mechanical modelling approach to the cooling and solidification phases associated with the shape casting of metals ei. Die, sand and investment casting. Novel vortex-based Finite Volume (FV) methods are described and employed with regard to the small strain, non-linear Computational Solid Mechanics (CSM) capabilities required to model shape casting. The CSM capabilities include the non-linear material phenomena of creep and thermo-elasto-visco-plasticity at high temperatures and thermo-elasto-visco-plasticity at low temperatures and also multi body deformable contact with which can occur between the metal casting of the mould. The vortex-based FV methods, which can be readily applied to unstructured meshes, are included within a comprehensive FV modelling framework, PHYSICA. The additional heat transfer, by conduction and convection, filling, porosity and solidification algorithms existing within PHYSICA for the complete modelling of all shape casting process employ cell-centred FV methods. The termo-mechanical coupling is performed in a staggered incremental fashion, which addresses the possible gap formation between the component and the mould, and is ultimately validated against a variety of shape casting benchmarks.

Structural characterisation and environmental application of organoclays for the removal of phenolic compounds

Modified montmorillonite was prepared at different surfactant (HDTMA) loadings through ion exchange. The conformational arrangement of the loaded surfactants within the interlayer space of MMT was obtained by computational modelling. The conformational change of surfactant molecules enhance the visual understanding of the results obtained from characterization methods such as XRD and surface analysis of the organoclays. Batch experiments were carried out for the adsorption of p-chlorophenol (PCP) and different conditions (pH and temperature) were used in order to determine the optimum sorption. For comparison purpose, the experiments were repeated under the same conditions for p-nitrophenol (PNP). Langmuir and Freundlich equations were applied to the adsorption isotherm of PCP and PNP. The Freundlich isotherm model was found to be the best fit for both of the phenolic compounds. This involved multilayer adsorptions in the adsorption process. In particular, the binding affinity value of PNP was higher than that of PCP and this is attributable to their hydrophobicities. The adsorption of the phenolic compounds by organoclays intercalated with highly loaded surfactants was markedly improved possibly due to the fact that the intercalated surfactant molecules within the interlayer space contribute to the partition phases, which result in greater adsorption of the organic pollutants.

Formation of neutral molecules of potential stellar interest by neutralisation of negative ions in a mass spectrometer - The application of experiment and molecular modelling in concert

This paper is a modified version of a lecture which describes the synthesis, structure and reactivity of some neutral molecules of stellar significance. The neutrals are formed in the collision cell of a mass spectrometer following vertical Franck-Condon one electron oxidation of anions of known bond connectivity. Neutrals are characterised by conversion to positive ions and by extensive theoretical studies at the CCSD(T)/aug-cc-pVDZ//B3LYP/6-31G(d) level of theory. Four systems are considered in detail, viz (i) the formation of linear C-4 and its conversion to the rhombus C-4, (ii) linear C-5 and the atom scrambling of this system when energised, (iii) the stable cumulene oxide CCCCCO, and (iv) the elusive species O2C-CO. This paper is not intended to be a review of interstellar chemistry: examples are selected from our own work in this area. (C) 2002 Elsevier Science Inc. All rights reserved.

Docking, molecular dynamics and QM/MM studies to delineate the mode of binding of CucurbitacinE to F-actin

CucurbitacinE (CurE) has been known to bind covalently to F-actin and inhibit depolymerization. However, the mode of binding of CurE to F-actin and the consequent changes in the F-actin dynamics have not been studied. Through quantum mechanical/molecular mechanical (QM/MM) and density function theory (DFT) simulations after the molecular dynamics (MD) simulations of the docked complex of F-actin and CurE, a detailed transition state (TS) model for the Michael reaction is proposed. The TS model shows nucleophilic attack of the sulphur of Cys257 at the beta-carbon of Michael Acceptor of CurE producing an enol intermediate that forms a covalent bond with CurE. The MD results show a clear difference between the structure of the F-actin in free form and F-actin complexed with CurE. CurE affects the conformation of the nucleotide binding pocket increasing the binding affinity between F-actin and ADP, which in turn could affect the nucleotide exchange. CurE binding also limits the correlated displacement of the relatively flexible domain 1 of F-actin causing the protein to retain a flat structure and to transform into a stable ``tense'' state. This structural transition could inhibit depolymerization of F-actin. In conclusion, CurE allosterically modulates ADP and stabilizes F-actin structure, thereby affecting nucleotide exchange and depolymerization of F-actin. (C) 2015 Elsevier Inc. All rights reserved.

Modelling the behavior of solder joints for wafer level SiP

Design for manufacture of system-in-package (SiP) structures is dependent on a number of physical processes that affect the final quality of the package in terms of its performance and reliability. Solder joints are key structures in a SiP and their behavior can be the critical factor in terms of reliability. This paper discusses the results from a research programme on design for manufacturing of system in package (SiP) technologies. The focus of the paper is on thermo-mechanical modelling of solder joints. This includes the behavior of the joints during testing plus some important insights into the reflow process and how physical phenomena taking place at the assembly stage can affect solder joint behavior. Finite element analysis of a numerical model of an SiP structure with various design parameters is discussed. The goal of this analysis is to identify the most promising combination of design parameters which guarantee longer lifetime of the solder joints and hence the SiP component. The parameters that were studied are the size of the package (i.e. number of solder joints per row), the presence of the underfill and/or the reinforcement as well as the thickness of the passive die. Discussion was also provided on phenomena that take place during the reflow process where the solder joints are formed. In particular, the formation of intermetallics at the solder-pad interfaces

Modelling of nano-imprint forming process for the production of miniaturised 3D structures

Nano-imprint forming (NIF) as manufacturing technology is ideally placed to enable high resolution, low-cost and high-throughput fabrication of three-dimensional fine structures and the packaging of heterogeneous micro-systems (S.Y. Chou and P.R. Krauss, 1997). This paper details a thermo-mechanical modelling methodology for optimising this process for different materials used in components such as mini-fluidics and bio-chemical systems, optoelectronics, photonics and health usage monitoring systems (HUMS). This work is part of a major UK Grand Challenge project - 3D-Mintegration - which is aiming to develop modelling and design technologies for the next generation of fabrication, assembly and test processes for 3D-miniaturised systems.