Modeling intrinsic noise and delays in chemical kinetics of coupled autoregulated oscillating cells

Delays are an important feature in temporal models of genetic regulation due to slow biochemical processes, such as transcription and translation. In this paper, we show how to model intrinsic noise effects in a delayed setting by either using a delay stochastic simulation algorithm (DSSA) or, for larger and more complex systems, a generalized Binomial τ-leap method (Bτ-DSSA). As a particular application, we apply these ideas to modeling somite segmentation in zebra fish across a number of cells in which two linked oscillatory genes (her1 and her7) are synchronized via Notch signaling between the cells.

Efficient hybrid-game strategies coupled to evolutionary algorithms for robust multidisciplinary design optimization in aerospace engineering

A number of game strategies have been developed in past decades and used in the fields of economics, engineering, computer science, and biology due to their efficiency in solving design optimization problems. In addition, research in multiobjective and multidisciplinary design optimization has focused on developing a robust and efficient optimization method so it can produce a set of high quality solutions with less computational time. In this paper, two optimization techniques are considered; the first optimization method uses multifidelity hierarchical Pareto-optimality. The second optimization method uses the combination of game strategies Nash-equilibrium and Pareto-optimality. This paper shows how game strategies can be coupled to multiobjective evolutionary algorithms and robust design techniques to produce a set of high quality solutions. Numerical results obtained from both optimization methods are compared in terms of computational expense and model quality. The benefits of using Hybrid and non-Hybrid-Game strategies are demonstrated.

Adaptive wing/aerofoil design optimisation using MOEA coupled to uncertainty design method

The use of adaptive wing/aerofoil designs is being considered as promising techniques in aeronautic/aerospace since they can reduce aircraft emissions, improve aerodynamic performance of manned or unmanned aircraft. The paper investigates the robust design and optimisation for one type of adaptive techniques; Active Flow Control (AFC) bump at transonic flow conditions on a Natural Laminar Flow (NLF) aerofoil designed to increase aerodynamic efficiency (especially high lift to drag ratio). The concept of using Shock Control Bump (SCB) is to control supersonic flow on the suction/pressure side of NLF aerofoil: RAE 5243 that leads to delaying shock occurrence or weakening its strength. Such AFC technique reduces total drag at transonic speeds due to reduction of wave drag. The location of Boundary Layer Transition (BLT) can influence the position the supersonic shock occurrence. The BLT position is an uncertainty in aerodynamic design due to the many factors, such as surface contamination or surface erosion. The paper studies the SCB shape design optimisation using robust Evolutionary Algorithms (EAs) with uncertainty in BLT positions. The optimisation method is based on a canonical evolution strategy and incorporates the concepts of hierarchical topology, parallel computing and asynchronous evaluation. Two test cases are conducted; the first test assumes the BLT is at 45% of chord from the leading edge and the second test considers robust design optimisation for SCB at the variability of BLT positions and lift coefficient. Numerical result shows that the optimisation method coupled to uncertainty design techniques produces Pareto optimal SCB shapes which have low sensitivity and high aerodynamic performance while having significant total drag reduction.

Free convection heat transfer through coupled thermal boundary layers in a partitioned triangular enclosure

A numerical investigation has been carried out for the coupled thermal boundary layers on both sides of a partition placed in an isosceles triangular enclosure along its middle symmetric line. The working fluid is considered as air which is initially quiescent. A sudden temperature difference between two zones of the enclosure has been imposed to trigger the natural convection. It is anticipated from the numerical simulations that the coupled thermal boundary layers development adjacent to the partition undergoes three distinct stages; namely an initial stage, a transitional stage and a steady state stage. Time dependent features of the coupled thermal boundary layers as well as the overall natural convection flow in the partitioned enclosure have been discussed and compared with the non-partitioned enclosure. Moreover, heat transfer as a form of local and overall average Nusselt number through the coupled thermal boundary layers and the inclined walls is also examined. The details results will be discussed in the full paper.

Expression Pattern of the Alpha-Kafirin Promoter Coupled with a Signal Peptide from Sorghum bicolor L. Moench

Regulatory sequences with endosperm specificity are essential for foreign gene expression in the desired tissue for both grain quality improvement and molecular pharming. In this study, promoters of seed storage α-kafirin genes coupled with signal sequence (ss) were isolated from Sorghum bicolor L. Moench genomic DNA by PCR. The α-kafirin promoter (α-kaf) contains endosperm specificity-determining motifs, prolamin-box, the O2-box 1, CATC, and TATA boxes required for α-kafirin gene expression in sorghum seeds. The constructs pMB-Ubi-gfp and pMB-kaf-gfp were microprojectile bombarded into various sorghum and sweet corn explants. GFP expression was detected on all explants using the Ubi promoter but only in seeds for the α-kaf promoter. This shows that the α-kaf promoter isolated was functional and demonstrated seed-specific GFP expression. The constructs pMB-Ubi-ss-gfp and pMB-kaf-ss-gfp were also bombarded into the same explants. Detection of GFP expression showed that the signal peptide (SP)::GFP fusion can assemble and fold properly, preserving the fluorescent properties of GFP.

Impact and energy absorption of road safety barriers by coupled SPH/FEM

Road safety barriers are used to minimise the severity of road accidents and protect lives and property. There are several types of barrier in use today. This paper reports the initial phase of research carried out to study the impact response of portable water-filled barrier (PWFB) which has the potential to absorb impact energy and hence provide crash mitigation under low to moderate speeds. Current research on the impact and energy absorption capacity of water-filled road safety barriers is limited due to the complexity of fluid-structure interaction under dynamic impact. In this paper, a novel fluid-structure interaction method is developed based on the combination of Smooth Particle Hydrodynamics (SPH) and Finite Element Method (FEM). The sloshing phenomenon of water inside a PWFB is investigated to explore the energy absorption capacity of water under dynamic impact. It was found that water plays an important role in energy absorption. The coupling analysis developed in this paper will provide a platform to further the research in optimising the behaviour of the PWFB. The effect of the amount of water on its energy absorption capacity is investigated and the results have practical applications in the design of PWFBs.

The effect of ribbing on the energy flow between two rectangular plates coupled at right angle

This paper presents an analytical model to study the effect of stiffening ribs on vibration transmission between two rectangular plates coupled at right angle. Interesting wave attenuation patterns were observed by placing the stiffening rib either on the source or on the receiving plate. The result can be used to improve the understanding of vibration and for vibration control of more complex structures such as transformer tanks and machine covers.

A coupled SPH-DEM model for fluid and solid mechanics of apple parenchyma cells during drying

A coupled SPH-DEM based two-dimensional (2-D) micro-scale single cell model is developed to predict basic cell-level shrinkage effects of apple parenchyma cells during air drying. In this newly developed drying model, Smoothed Particle Hydrodynamics (SPH) is used to model the low Reynolds Number fluid motions of the cell protoplasm, and a Discrete Element Method (DEM) is employed to simulate the polymer-like cell wall. Simulations results reasonably agree with published experimental drying results on cellular shrinkage properties such as cellular area, diameter and perimeter. These preliminary results indicate that the model is effective for the modelling and simulation of apple parenchyma cells during air drying.

Critical timescales and time intervals for coupled linear processes

In 1991, McNabb introduced the concept of mean action time (MAT) as a finite measure of the time required for a diffusive process to effectively reach steady state. Although this concept was initially adopted by others within the Australian and New Zealand applied mathematics community, it appears to have had little use outside this region until very recently, when in 2010 Berezhkovskii and coworkers rediscovered the concept of MAT in their study of morphogen gradient formation. All previous work in this area has been limited to studying single–species differential equations, such as the linear advection–diffusion–reaction equation. Here we generalise the concept of MAT by showing how the theory can be applied to coupled linear processes. We begin by studying coupled ordinary differential equations and extend our approach to coupled partial differential equations. Our new results have broad applications including the analysis of models describing coupled chemical decay and cell differentiation processes, amongst others.

A coupled SPH/FEM analysis of portable water filled barriers

Portable water filled barriers (PWFB) are semi-rigid roadside barriers which have the potential to display good crash attenuation characteristics at low and moderate impact speeds. The traditional mesh based numerical methods alone fail to simulate this type of impact with precision, stability and efficiency. This paper proposes to develop an advanced simulation model based on the combination of Smoothed Particles Hydrodynamics (SPH), a meshless method, and finite element method (FEM) for fluid-structure analysis using the commercially available software package LS-Dyna. The interaction between SPH particles and FEA elements is studied in this paper. Two methods of element setup at the element boundary were investigated. The response of the impacted barrier and fluid inside were analysed and compared. The system response and lagging were observed and reported in this paper. It was demonstrated that coupled SPH/FEM can be used in full scale PWFB modelling application. This will aid the research in determining the best initial setup to couple FEA and SPH in road safety barrier for impact response and safety analysis in the future.

Deformation with coupled chemical diffusion

The deformation of rocks is commonly intimately associated with metamorphic reactions. This paper is a step towards understanding the behaviour of fully coupled, deforming, chemically reacting systems by considering a simple example of the problem comprising a single layer system with elastic-power law viscous constitutive behaviour where the deformation is controlled by the diffusion of a single chemical component that is produced during a metamorphic reaction. Analysis of the problem using the principles of non-equilibrium thermodynamics allows the energy dissipated by the chemical reaction-diffusion processes to be coupled with the energy dissipated during deformation of the layers. This leads to strain-rate softening behaviour and the resultant development of localised deformation which in turn nucleates buckles in the layer. All such diffusion processes, in leading to Herring-Nabarro, Coble or “pressure solution” behaviour, are capable of producing mechanical weakening through the development of a “chemical viscosity”, with the potential for instability in the deformation. For geologically realistic strain rates these chemical feed-back instabilities occur at the centimetre to micron scales, and so produce structures at these scales, as opposed to thermal feed-back instabilities that become important at the 100–1000 m scales.

First principle study of hydrogenation of MgB2 : an important step toward reversible hydrogen storage in the coupled LiBH4/MgH2 system

Recent experiments [F. E. Pinkerton, M. S. Meyer, G. P. Meisner, M. P. Balogh, and J. J. Vajo, J. Phys. Chem. C 111, 12881 (2007) and J. J. Vajo and G. L. Olson, Scripta Mater. 56, 829 (2007)] demonstrated that the recycling of hydrogen in the coupled LiBH4/MgH2 system is fully reversible. The rehydrogenation of MgB2 is an important step toward the reversibility. By using ab initio density functional theory calculations, we found that the activation barrier for the dissociation of H2 are 0.49 and 0.58 eV for the B and Mg-terminated MgB2(0001) surface, respectively. This implies that the dissociation kinetics of H2 on a MgB2 (0001) surface should be greatly improved compared to that in pure Mg materials. Additionally, the diffusion of dissociated H atom on the Mg-terminated MgB2(0001) surface is almost barrier-less. Our results shed light on the experimentally-observed reversibility and improved kinetics for the coupled LiBH4/MgH2 system.

Metabolomics coupled with proteomics advancing drug discovery toward more agile development of targeted combination therapies

To enhance the therapeutic efficacy and reduce the adverse effects of traditional Chinese medicine, practitioners often prescribe combinations of plant species and/or minerals, called formulae. Unfortunately, the working mechanisms of most of these compounds are difficult to determine and thus remain unknown. In an attempt to address the benefits of formulae based on current biomedical approaches, we analyzed the components of Yinchenhao Tang, a classical formula that has been shown to be clinically effective for treating hepatic injury syndrome. The three principal components of Yinchenhao Tang are Artemisia annua L., Gardenia jasminoids Ellis, and Rheum Palmatum L., whose major active ingredients are 6,7-dimethylesculetin (D), geniposide (G), and rhein (R), respectively. To determine the mechanisms underlying the efficacy of this formula, we conducted a systematic analysis of the therapeutic effects of the DGR compound using immunohistochemistry, biochemistry, metabolomics, and proteomics. Here, we report that the DGR combination exerts a more robust therapeutic effect than any one or two of the three individual compounds by hitting multiple targets in a rat model of hepatic injury. Thus, DGR synergistically causes intensified dynamic changes in metabolic biomarkers, regulates molecular networks through target proteins, has a synergistic/additive effect, and activates both intrinsic and extrinsic pathways.