Correlating flow induced shear stress and chondrocytes activity in micro-porous scaffold using computational fluid dynamics and rapid prototyping

Flow induced shear stress plays an important role in regulating cell growth and distribution in scaffolds. This study sought to correlate wall shear stress and chondrocytes activity for engineering design of micro-porous osteochondral grafts based on the hypothesis that it is possible to capture and discriminate between the transmitted force and cell response at the inner irregularities. Unlike common tissue engineering therapies with perfusion bioreactors in which flow-mediated stress is the controlling parameter, this work assigned the associated stress as a function of porosity to influence in vitro proliferation of chondrocytes. D-optimality criterion was used to accommodate three pore characteristics for appraisal in a mixed level fractional design of experiment (DOE); namely, pore size (4 levels), distribution pattern (2 levels) and density (3 levels). Micro-porous scaffolds (n=12) were fabricated according to the DOE using rapid prototyping of an acrylic-based bio-photopolymer. Computational fluid dynamics (CFD) models were created correspondingly and used on an idealized boundary condition with a Newtonian fluid domain to simulate the dynamic microenvironment inside the pores. In vitro condition was reproduced for the 3D printed constructs seeded by high pellet densities of human chondrocytes and cultured for 72 hours. The results showed that cell proliferation was significantly different in the constructs (p<0.05). Inlet fluid velocity of 3×10-2mms-1 and average shear stress of 5.65×10-2 Pa corresponded with increased cell proliferation for scaffolds with smaller pores in hexagonal pattern and lower densities. Although the analytical solution of a Poiseuille flow inside the pores was found insufficient for the description of the flow profile probably due to the outside flow induced turbulence, it showed that the shear stress would increase with cell growth and decrease with pore size. This correlation demonstrated the basis for determining the relation between the induced stress and chondrocyte activity to optimize microfabrication of engineered cartilaginous constructs.

Electrocatalytically switchable CO2 capture : first principle computational exploration of carbon nanotubes with pyridinic nitrogen

Carbon nanotubes with specific nitrogen doping are proposed for controllable, highly selective, and reversible CO2 capture. Using density functional theory incorporating long-range dispersion corrections, we investigated the adsorption behavior of CO2 on (7,7) single-walled carbon nanotubes (CNTs) with several nitrogen doping configurations and varying charge states. Pyridinic-nitrogen incorporation in CNTs is found to induce an increasing CO2 adsorption strength with electron injecting, leading to a highly selective CO2 adsorption in comparison with N2. This functionality could induce intrinsically reversible CO2 adsorption as capture/release can be controlled by switching the charge carrying state of the system on/off. This phenomenon is verified for a number of different models and theoretical methods, with clear ramifications for the possibility of implementation with a broader class of graphene-based materials. A scheme for the implementation of this remarkable reversible electrocatalytic CO2-capture phenomenon is considered.

A computational study of carbon dioxide adsorption on solid boron

Capturing and sequestering carbon dioxide (CO2) can provide a route to partial mitigation of climate change associated with anthropogenic CO2 emissions. Here we report a comprehensive theoretical study of CO2 adsorption on two phases of boron, α-B12 and γ-B28. The theoretical results demonstrate that the electron deficient boron materials, such as α-B12 and γ-B28, can bond strongly with CO2 due to Lewis acid-base interactions because the electron density is higher on their surfaces. In order to evaluate the capacity of these boron materials for CO2 capture, we also performed calculations with various degrees of CO2 coverage. The computational results indicate CO2 capture on the boron phases is a kinetically and thermodynamically feasible process, and therefore from this perspective these boron materials are predicted to be good candidates for CO2 capture.

Reaction of Aromatic Peroxyl Radicals with Alkynes: A Mass Spectrometric and Computational Study Using the Distonic Radical Ion Approach

The reaction of the aromatic distonic peroxyl radical cations N-methyl pyridinium-4-peroxyl (PyrOO center dot+) and 4-(N,N,N-trimethyl ammonium)-phenyl peroxyl (AnOO center dot+), with symmetrical dialkyl alkynes 10?ac was studied in the gas phase by mass spectrometry. PyrOO center dot+ and AnOO center dot+ were produced through reaction of the respective distonic aryl radical cations Pyr center dot+ and An center dot+ with oxygen, O2. For the reaction of Pyr center dot+ with O2 an absolute rate coefficient of k1=7.1X10-12 cm3 molecule-1 s-1 and a collision efficiency of 1.2?% was determined at 298 K. The strongly electrophilic PyrOO center dot+ reacts with 3-hexyne and 4-octyne with absolute rate coefficients of khexyne=1.5X10-10 cm3 molecule-1 s-1 and koctyne=2.8X10-10 cm3 molecule-1 s-1, respectively, at 298 K. The reaction of both PyrOO center dot+ and AnOO center dot+ proceeds by radical addition to the alkyne, whereas propargylic hydrogen abstraction was observed as a very minor pathway only in the reactions involving PyrOO center dot+. A major reaction pathway of the vinyl radicals 11 formed upon PyrOO center dot+ addition to the alkynes involves gamma-fragmentation of the peroxy O?O bond and formation of PyrO center dot+. The PyrO center dot+ is rapidly trapped by intermolecular hydrogen abstraction, presumably from a propargylic methylene group in the alkyne. The reaction of the less electrophilic AnOO center dot+ with alkynes is considerably slower and resulted in formation of AnO center dot+ as the only charged product. These findings suggest that electrophilic aromatic peroxyl radicals act as oxygen atom donors, which can be used to generate alpha-oxo carbenes 13 (or isomeric species) from alkynes in a single step. Besides gamma-fragmentation, a number of competing unimolecular dissociative reactions also occur in vinyl radicals 11. The potential energy diagrams of these reactions were explored with density functional theory and ab initio methods, which enabled identification of the chemical structures of the most important products.

A comparison of the gas phase acidities of phospholipid headgroups: Experimental and computational studies

Proton-bound dimers consisting of two glycerophospholipids with different headgroups were prepared using negative ion electrospray ionization and dissociated in a triple quadrupole mass spectrometer. Analysis of the tandem mass spectra of the dimers using the kinetic method provides, for the first time, an order of acidity for the phospholipid classes in the gas phase of PE < PA << PG < PS < PI. Hybrid density functional calculations on model phospholipids were used to predict the absolute deprotonation enthalpies of the phospholipid classes from isodesmic proton transfer reactions with phosphoric acid. The computational data largely support the experimental acidity trend, with the exception of the relative acidity ranking of the two most acidic phospholipid species. Possible causes of the discrepancy between experiment and theory are discussed and the experimental trend is recommended. The sequence of gas phase acidities for the phospholipid headgroups is found to (1) have little correlation with the relative ionization efficiencies of the phospholipid classes observed in the negative ion electrospray process, and (2) correlate well with fragmentation trends observed upon collisional activation of phospholipid \[M - H](-) anions. (c) 2005 American Society for Mass Spectrometry.

Part 1 MOO methods for multidisciplinary design using parallel evolutionary algorithms, game theory and hierarchical topology. (Part 1.) Theoretical aspects

Two lecture notes describe recent developments of evolutionary multi objective optimization (MO) techniques in detail and their advantages and drawbacks compared to traditional deterministic optimisers. The role of Game Strategies (GS), such as Pareto, Nash or Stackelberg games as companions or pre-conditioners of Multi objective Optimizers is presented and discussed on simple mathematical functions in Part I , as well as their implementations on simple aeronautical model optimisation problems on the computer using a friendly design framework in Part II. Real life (robust) design applications dealing with UAVs systems or Civil Aircraft and using the EAs and Game Strategies combined material of Part I & Part II are solved and discussed in Part III providing the designer new compromised solutions useful to digital aircraft design and manufacturing. Many details related to Lectures notes Part I, Part II and Part III can be found by the reader in [68].

Two-scale computational modelling of unsaturated flow in soils exhibiting small scale heterogeneities

Unsaturated water flow in soil is commonly modelled using Richards’ equation, which requires the hydraulic properties of the soil (e.g., porosity, hydraulic conductivity, etc.) to be characterised. Naturally occurring soils, however, are heterogeneous in nature, that is, they are composed of a number of interwoven homogeneous soils each with their own set of hydraulic properties. When the length scale of these soil heterogeneities is small, numerical solution of Richards’ equation is computationally impractical due to the immense effort and refinement required to mesh the actual heterogeneous geometry. A classic way forward is to use a macroscopic model, where the heterogeneous medium is replaced with a fictitious homogeneous medium, which attempts to give the average flow behaviour at the macroscopic scale (i.e., at a scale much larger than the scale of the heterogeneities). Using the homogenisation theory, a macroscopic equation can be derived that takes the form of Richards’ equation with effective parameters. A disadvantage of the macroscopic approach, however, is that it fails in cases when the assumption of local equilibrium does not hold. This limitation has seen the introduction of two-scale models that include at each point in the macroscopic domain an additional flow equation at the scale of the heterogeneities (microscopic scale). This report outlines a well-known two-scale model and contributes to the literature a number of important advances in its numerical implementation. These include the use of an unstructured control volume finite element method and image-based meshing techniques, that allow for irregular micro-scale geometries to be treated, and the use of an exponential time integration scheme that permits both scales to be resolved simultaneously in a completely coupled manner. Numerical comparisons against a classical macroscopic model confirm that only the two-scale model correctly captures the important features of the flow for a range of parameter values.

Computational aspects of probabilistic assessment of UAS robust autonomy

As the level of autonomy in Unmanned Aircraft Systems (UAS) increases, there is an imperative need for developing methods to assess robust autonomy. This paper focuses on the computations that lead to a set of measures of robust autonomy. These measures are the probabilities that selected performance indices related to the mission requirements and airframe capabilities remain within regions of acceptable performance.

A SiC-based matrix converter topology for inductive power transfer system

Typical inductive power transfer (IPT) systems employ two power conversion stages to generate a high-frequency primary current from low-frequency utility supply. This paper proposes a matrix-converter-based IPT system, which employs high-speed SiC devices to facilitate the generation of high-frequency current through a single power conversion stage. The proposed matrix converter topology transforms a three-phase low-frequency voltage system to a high-frequency single-phase voltage, which, in turn, powers a series compensated IPT system. A comprehensive mathematical model is developed and power losses are evaluated to investigate the efficiency of the proposed converter topology. Theoretical results are presented with simulations, which are performed in MATLAB/Simulink, in comparison to a conventional two-stage converter. Experimental evident of a prototype IPT system is also presented to demonstrate the applicability of the proposed concept.

Fragmentations of deprotonated alkyl hydroperoxides (ROO-) upon collisional activation : A combined experimental and computational study

The collision-induced dissociation ( CID) mass spectra of the \[M-H](-) anions of methyl, ethyl, and tert-butyl hydroperoxides have been measured over a range of collision energies in a flowing afterglow - selected ion flow tube (FA-SIFT) mass spectrometer. Activation of the CH3OO- anion is found to give predominantly HO- fragment anions whilst CH3CH2OO- and (CH3)(3)COO- produce HOO- as the major ionic fragment. These results, and other minor fragmentation pathways, can be rationalized in terms of unimolecular rearrangement of the activated anions with subsequent decomposition. The rearrangement reactions occur via initial abstraction of a proton from the alpha-carbon in the case of CH3OO- or the beta-carbon for CH3CH2OO- and (CH3)(3)COO-. Electronic structure calculations suggest that for the CH3CH2OO- anion, which can theoretically undergo both alpha- and beta-proton abstraction, the latter pathway, resulting in HOO- + CH2CH2, is energetically preferred.

Undulating matter : a topology of the studio

With specific reference to the writing of Dan Graham and the experiences of creative practice, this paper will elaborate an account of studio practice as a topology - a theory drawn from mathematics in which space is understood not as a static field but in terms of properties of connectedness, movement and differentiation. This paper will trace a brief sequence of topological formulations to draw together the expression of topology as form and its structural dimension as a methodology in the specific context of the author’s studio practice. In so doing, this paper seeks to expand the notion of topology in art beyond its association with Conceptual Art of the 1960s and 70s to propose that topology provides a dynamic theoretical model for apprehending the generative ‘logic’ that gives direction and continuity to the art-making process.

Half-wave cycloconverter-based photovoltaic microinverter topology with phase-shift power modulation

A grid-connected microinverter with a reduced number of power conversion stages and fewer passive components is proposed. A high-frequency transformer and a series-resonant tank are used to interface the full-bridge inverter to the half-wave cycloconverter. All power switches are switched with zero-voltage switching. Phase-shift power modulation is used to control the output power of the inverter. A steady-state analysis of the proposed topology is presented to determine the average output power of the inverter. Analysis of soft switching of the full-bridge and the half-wave cycloconverter is presented with respect to voltage gain, quality factor, and phase shift of the inverter. Simulation and experimental results are presented to validate the operation of the proposed topology.

Computational science for undergraduate biologists via QUT.Bio.Excel

Molecular biology is a scientific discipline which has changed fundamentally in character over the past decade to rely on large scale datasets – public and locally generated - and their computational analysis and annotation. Undergraduate education of biologists must increasingly couple this domain context with a data-driven computational scientific method. Yet modern programming and scripting languages and rich computational environments such as R and MATLAB present significant barriers to those with limited exposure to computer science, and may require substantial tutorial assistance over an extended period if progress is to be made. In this paper we report our experience of undergraduate bioinformatics education using the familiar, ubiquitous spreadsheet environment of Microsoft Excel. We describe a configurable extension called QUT.Bio.Excel, a custom ribbon, supporting a rich set of data sources, external tools and interactive processing within the spreadsheet, and a range of problems to demonstrate its utility and success in addressing the needs of students over their studies.

Modelling of arc welding : the importance of including the arc plasma in the computational domain

We present results of computational simulations of tungsten-inert-gas and metal-inert-gas welding. The arc plasma and the electrodes (including the molten weld pool when necessary) are included self-consistently in the computational domain. It is shown, using three examples, that it would be impossible to accurately estimate the boundary conditions on the weld-pool surface without including the arc plasma in the computational domain. First, we show that the shielding gas composition strongly affects the properties of the arc that influence the weld pool: heat flux density, current density, shear stress and arc pressure at the weld-pool surface. Demixing is found to be important in some cases. Second, the vaporization of the weld-pool metal and the diffusion of the metal vapour into the arc plasma are found to decrease the heat flux density and current density to the weld pool. Finally, we show that the shape of the wire electrode in metal-inert-gas welding has a strong influence on flow velocities in the arc and the pressure and shear stress at the weld-pool surface. In each case, we present evidence that the geometry and depth of the weld pool depend strongly on the properties of the arc.