Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms.

X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to structure. In practice, the crystallization process proceeds through knowledge-informed empiricism. Better physico-chemical understanding remains elusive because of the large number of variables involved, hence little guidance is available to systematically identify solution conditions that promote crystallization. To help determine relationships between macromolecular properties and their crystallization propensity, we have trained statistical models on samples for 182 proteins supplied by the Northeast Structural Genomics consortium. Gaussian processes, which capture trends beyond the reach of linear statistical models, distinguish between two main physico-chemical mechanisms driving crystallization. One is characterized by low levels of side chain entropy and has been extensively reported in the literature. The other identifies specific electrostatic interactions not previously described in the crystallization context. Because evidence for two distinct mechanisms can be gleaned both from crystal contacts and from solution conditions leading to successful crystallization, the model offers future avenues for optimizing crystallization screens based on partial structural information. The availability of crystallization data coupled with structural outcomes analyzed through state-of-the-art statistical models may thus guide macromolecular crystallization toward a more rational basis.

A finite volume unstructured mesh approach to dynamic fluid-structure interaction: an assessment of the challenge of flutter analysis

Computational modelling of dynamic fluid-structure interaction (DFSI) is problematical since conventionally computational fluid dynamics (CFD) is solved using finite volume (FV) methods and computational structural mechanics (CSM) is based entirely on finite element (FE) methods. Hence, progress in modelling the emerging multi-physics problem of dynamic fluid-structure interaction in a consistent manner is frustrated and significant problems in computation convergence may be encountered in transferring and filtering data from one mesh and solution procedure to another, unless the fluid-structure coupling is either one way, very weak or both. This paper sets out the solution procedure for modelling the multi-physics dynamic fluid-structure interaction problem within a single software framework PHYSICA, using finite volume, unstructured mesh (FV-UM) procedures and will focus upon some of the problems and issues that have to be resolved for time accurate closely coupled dynamic fluid-structure flutter analysis.

A computational model of coupled heat and moisture transfer with phase change in granular sugar during varying environmental conditions

As part of a comprehensive effort to predict the development of caking in granular materials, a mathematical model is introduced to model simultaneous heat and moisture transfer with phase change in porous media when undergoing temperature oscillations/cycling. The resulting model partial differential equations were solved using finite-volume procedures in the context of the PHYSICA framework and then applied to the analysis of sugar in storage. The influence of temperature on absorption/desorption and diffusion coefficients is coupled into the transport equations. The temperature profile, the depth of penetration of the temperature oscillation into the bulk solid, and the solids moisture content distribution were first calculated, and these proved to be in good agreement with experimental data. Then, the influence of temperature oscillation on absolute humidity, moisture concentration, and moisture migration for different parameters and boundary conditions was examined. As expected, the results show that moisture near boundary regions responds faster than farther away from them with surface temperature changes. The moisture absorption and desorption in materials occurs mainly near boundary regions (where interactions with the environment are more pronounced). Small amounts of solids moisture content, driven by both temperature and vapour concentration gradients, migrate between boundary and center with oscillating temperature.

Nonlinear MHD stability of aluminium reduction cells

An industrial electrolysis cell used to produce primary aluminium is sensitive to waves at the interface of liquid aluminium and electrolyte. The interface waves are similar to stratified sea layers [1], but the penetrating electric current and the associated magnetic field are intricately involved in the oscillation process, and the observed wave frequencies are shifted from the purely hydrodynamic ones [2]. The interface stability problem is of great practical importance because the electrolytic aluminium production is a major electrical energy consumer, and it is related to environmental pollution rate. The stability analysis was started in [3] and a short summary of the main developments is given in [2]. Important aspects of the multiple mode interaction have been introduced in [4], and a widely used linear friction law first applied in [5]. In [6] a systematic perturbation expansion is developed for the fluid dynamics and electric current problems permitting reduction of the three-dimensional problem to a two dimensional one. The procedure is more generally known as “shallow water approximation” which can be extended for the case of weakly non-linear and dispersive waves. The Boussinesq formulation permits to generalise the problem for non-unidirectionally propagating waves accounting for side walls and for a two fluid layer interface [1]. Attempts to extend the electrolytic cell wave modelling to the weakly nonlinear case have started in [7] where the basic equations are derived, including the nonlinearity and linear dispersion terms. An alternative approach for the nonlinear numerical simulation for an electrolysis cell wave evolution is attempted in [8 and references there], yet, omitting the dispersion terms and without a proper account for the dissipation, the model can predict unstable waves growth only. The present paper contains a generalisation of the previous non linear wave equations [7] by accounting for the turbulent horizontal circulation flows in the two fluid layers. The inclusion of the turbulence model is essential in order to explain the small amplitude self-sustained oscillations of the liquid metal surface observed in real cells, known as “MHD noise”. The fluid dynamic model is coupled to the extended electromagnetic simulation including not only the fluid layers, but the whole bus bar circuit and the ferromagnetic effects [9].

An analysis of a microfabricated solenoid inductor

A microscale solenoid inductor is manufactured using electrodeposition method. The inductor is designed for switching mode DC-DC converters operating at switching frequencies in the mega-Hertz range. Two magnetic core materials, electroformed permalloy Ni80 Fe20 film and Vitrovac 6025 which is a commercial magnetic film, have been analyzed using experimental and computer modeling techniques

An analysis of the changes to the mechanical and acoustical properties of paper caused by the damage mechanisms present in the fibre structure

This paper will analyse two of the likely damage mechanisms present in a paper fibre matrix when placed under controlled stress conditions: fibre/fibre bond failure and fibre failure. The failure process associated with each damage mechanism will be presented in detail focusing on the change in mechanical and acoustic properties of the surrounding fibre structure before and after failure. To present this complex process mathematically, geometrically simple fibre arrangements will be chosen based on certain assumptions regarding the structure and strength of paper, to model the damage mechanisms. The fibre structures are then formulated in terms of a hybrid vibro-acoustic model based on a coupled mass/spring system and the pressure wave equation. The model will be presented in detail in the paper. The simulation of the simple fibre structures serves two purposes; it highlights the physical and acoustic differences of each damage mechanism before and after failure, and also shows the differences in the two damage mechanisms when compared with one another. The results of the simulations are given in the form of pressure wave contours, time-frequency graphs and the Continuous Wavelet Transform (CWT) diagrams. The analysis of the results leads to criteria by which the two damage mechanisms can be identified. Using these criteria it was possible to verify the results of the simulations against experimental acoustic data. The models developed in this study are of specific practical interest in the paper-making industry, where acoustic sensors may be used to monitor continuous paper production. The same techniques may be adopted more generally to correlate acoustic signals to damage mechanisms in other fibre-based structures.

Coupled FDTD-FVM simulation of microwave heating of polymer materials for micro-systems packaging applications

Heating in an idealised polymer load in a novel open-ended variable frequency microwave oven is numerically simulated using a couple solver approach. The frequency-agile microwave oven bonding system (FAMOBS)is developed to meet rapid polymer curing requirements in microelectronics and optoelectronics manufacturing. The heating of and idealised polymer load has been investigated through numerical modelling. Assessment of the system comprises of simulation of electromagnetic fields and of temperature distribution within the load. Initial simulation results are presented and contrasted with experimental analysis of field distribution

Reliability analysis of SiP structures

This presentation discusses latest developments in SiP technology and the challenges for design in terms of manufacture and reliability. It presents results from a UK government funded project that aims to develop modelling techniques that will assess the thermo-mechanical reliability of SiP structures such as (i) stacked die, (ii) side-by-side dies and (iii) embedded die. Finite element analysis coupled with numerical optimisation and uncertainty analysis is used is used to model the reliability of a particular package design. In particular, the damage (energy density) in the lead free solder interconnects under accelerated temperature cycling is predicted and used to observe the fatigue life-time. Warpage of the structure is also investigated

Numerical analysis of thermal stresses induced during VFM encapsulant curing

Encapsulant curing using a Variable Frequency Microwave (VFM) system is analysed numerically. Thermosetting polymer encapsulant materials require an input of heat energy to initiate the cure process. In this article, the heating is considered to be performed by a novel microwave system, able to perform the curing process more rapidly than conventional techniques. Thermal stresses are induced when packages containing materials with differing coefficients of thermal expansion are heated, and cure stresses are induced as thermosetting polymer materials shrink during the cure process. These stresses are developed during processing and remain as residual stresses within the component after the manufacturing process is complete. As residual stresses will directly affect the reliability of the device, it is necessary to assess their magnitude and the effect on package reliability. A coupled multiphysics model has been developed to numercially analyse the microwave curing process. In order to obtain a usefully accurate model of this process, a holistic approach has been taken, in which the process is not considered to be a sequence of discrete steps, but as a complex coupled system. An overview of the implemented numerical model is presented, with particular focus paid to analysis of induced thermal stresses. Results showing distribution of stresses within an idealised microelectronics package are presented and discussed.

Multiphysics simulation of microwave processing using a multidomain coupled solver approach

Microwave processing of materials is numerically simulated using a coupled solver approach. Microwave heating is a complex coupled process due to the variation in dielectric properties during heating. The effects of heating an object in a electromagnetic field directly influence the manner in which it interacts with the field. Simplifying assumptions and empirical solutions do not capture the fundamental physics involved and, in general, do not provide usefully accurate solutions in a number of practical problems. In order to capture the underlying processes involved in microwave heating, the problem must be looked at in a holistic manner rather than a number of discrete processes. This contribution outlines a coupled-solver multiphysics analysis approach to the solution of practical microwave heating problems.

Role of bonding time and temperature on the physical properties of coupled anisotropic conductive–nonconductive adhesive film for flip chip on glass technology

Using thermosetting epoxy based conductive adhesive films for the flip chip interconnect possess a great deal of attractions to the electronics manufacturing industries due to the ever increasing demands for miniaturized electronic products. Adhesive manufacturers have taken many attempts over the last decade to produce a number of types of adhesives and the coupled anisotropic conductive-nonconductive adhesive film is one of them. The successful formation of the flip chip interconnection using this particular type of adhesive depends on, among factors, how the physical properties of the adhesive changes during the bonding process. Experimental measurements of the temperature in the adhesive have revealed that the temperature becomes very close to the required maximum bonding temperature within the first 1s of the bonding time. The higher the bonding temperature the faster the ramp up of temperature is. A dynamic mechanical analysis (DMA) has been carried out to investigate the nature of the changes of the physical properties of the coupled anisotropic conductive-nonconductive adhesive film for a range of bonding parameters. Adhesive samples that are pre-cured at 170, 190 and 210°C for 3, 5 and 10s have been analyzed using a DMA instrument. The results have revealed that the glass transition temperature of this type of adhesive increases with the increase in the bonding time for the bonding temperatures that have been used in this work. For the curing time of 3 and 5s, the maximum glass transition temperature increases with the increase in the bonding temperature, but for the curing time of 10s the maximum glass transition temperature has been observed in the sample which is cured at 190°C. Based on these results it has been concluded that the optimal bonding temperature and time for this kind of adhesive are 190°C and 10s, respectively.

Numerical optimisation techniques applied to evacuation analysis

A common problem faced by fire safety engineers in the field of evacuation analysis concerns the optimal design of an arbitrarily complex structure in order to minimise evacuation times. How does the engineer determine the best solution? In this study we introduce the concept of numerical optimisation techniques to address this problem. The study makes user of the buildingEXODUS evacuation model coupled with classical optimisation theory including Design of Experiments (DoE) and Response Surface Models (RSM). We demonstrate the technique using a relatively simple problem of determining the optimal location for a single exit in a square room.

Vulnerability of coastal ecosystems to changes in harmful algal bloom distribution in response to climate change: projections based on model analysis

Harmful algal blooms (HABs), those proliferations of algae that can cause fish kills, contaminate seafood with toxins, form unsightly scums, or detrimentally alter ecosystem function have been increasing in frequency, magnitude, and duration worldwide. Here, using a global modeling approach, we show, for three regions of the globe, the potential effects of nutrient loading and climate change for two HAB genera, pelagic Prorocentrum and Karenia, each with differing physiological characteristics for growth. The projections (end of century, 2090-2100) are based on climate change resulting from the A1B scenario of the Intergovernmental Panel on Climate Change Institut Pierre Simon Laplace Climate Model (IPCC, IPSL-CM4), applied in a coupled oceanographic-biogeochemical model, combined with a suite of assumed physiological 'rules' for genera-specific bloom development. Based on these models, an expansion in area and/or number of months annually conducive to development of these HABs along the NW European Shelf-Baltic Sea system and NE Asia was projected for both HAB genera, but no expansion (Prorocentrum spp.), or actual contraction in area and months conducive for blooms (Karenia spp.), was projected in the SE Asian domain. The implications of these projections, especially for Northern Europe, are shifts in vulnerability of coastal systems to HAB events, increased regional HAB impacts to aquaculture, increased risks to human health and ecosystems, and economic consequences of these events due to losses to fisheries and ecosystem services.

Rational design of a dual-mode optical and chemical prodrug

Purpose. The purpose of this study is to demonstrate the rational design and behaviour of the first dual mode optical and chemical prodrug, exemplified by an acetyl salicylic acid-based system. Methods. A cyclic 1,4-benzodioxinone prodrug was synthesised by reaction of 3,5-dimethoxybenzoin and acetyl salicoyl chloride with pyridine. After purification by column chromatography and recrystallization, characterization was achieved using infrared and NMR spectroscopies, mass spectrometry, elemental analysis and single crystal X-ray diffraction. Light-triggered drug liberation was characterised via UV-visible spectroscopy following low-power 365 nm irradiation for controlled times. Chemical drug liberation was characterised via UV-visible spectroscopy in pH 5.5 solution. Results. The synthetic method yielded pure prodrug, with full supporting characterisation. Light-triggered drug liberation proceeded at a rate of 8.30 10j2 sj1, while chemical, hydrolytic liberation proceeded independently at 1.89 10j3 sj1. The photochemical and hydrolytic reactions were both quantitative. Conclusions. This study demonstrates the first rational dual-mode optical and chemical prodrug, using acetyl salicylic acid as a model, acting as a paradigm for future dual-mode systems. Photochemical drug liberation proceeds 44 times faster than chemical liberation, suggesting potential use in drug-eluting medical devices where an additional burst of drug is required at the onset of infection.