Some practical issues in the design and analysis of computer experiments

Deterministic computer simulations of physical experiments are now common techniques in science and engineering. Often, physical experiments are too time consuming, expensive or impossible to conduct. Complex computer models or codes, rather than physical experiments lead to the study of computer experiments, which are used to investigate many scientific phenomena of this nature. A computer experiment consists of a number of runs of the computer code with different input choices. The Design and Analysis of Computer Experiments is a rapidly growing technique in statistical experimental design. This thesis investigates some practical issues in the design and analysis of computer experiments and attempts to answer some of the questions faced by experimenters using computer experiments. In particular, the question of the number of computer experiments and how they should be augmented is studied and attention is given to when the response is a function over time.

Dynamic virtual fences for controlling cows

A virtual fence is created by applying an aversive stimulus to an animal when it approaches a predefined boundary. It is implemented by a small animal-borne computer system with a GPS receiver. This approach allows the implementation of virtual paddocks inside a normal physically-fenced paddock. Since the fence lines are virtual they can be moved by programming to meet the needs of animal or land management. This approach enables us to consider animals as agents with natural mobility that are controllable and to apply a vast body of theory in motion planning. In this paper we describe a herd-animal simulator and physical experiments conducted on a small herd of 10 animals using a Smart Collar. The Smart Collar consists of a GPS, PDA, wireless networking and a sound amplifier. We describe a motion planning algorithm that can move a virtual paddock subject to landscape constraints which is suitable for mustering cows. We present simulation results and data from experiments with 8 cows equipped with Smart Collars.

Coordinating aerial robots and sensor networks for localization and navigation

We consider multi-robot systems that include sensor nodes and aerial or ground robots networked together. We describe two cooperative algorithms that allow robots and sensors to enhance each other's performance. In the first algorithm, an aerial robot assists the localization of the sensors. In the second algorithm, a localized sensor network controls the navigation of an aerial robot. We present physical experiments with an flying robot and a large Mica Mote sensor network.

Computer experiment – a case study for modelling and simulation of manufacturing systems

Deterministic computer simulation of physical experiments is now a common technique in science and engineering. Often, physical experiments are too time consuming, expensive or impossible to conduct. Complex computer models or codes, rather than physical experiments lead to the study of computer experiments, which are used to investigate many scientific phenomena. A computer experiment consists of a number of runs of the computer code with different input choices. The Design and Analysis of Computer Experiments is a rapidly growing technique in statistical experimental design. This paper aims to discuss some practical issues when designing a computer simulation and/or experiments for manufacturing systems. A case study approach is reviewed and presented.

Cell type-dependent, infection-induced, aberrant DNA methylation in gastric cancer

Epigenetic changes correspond to heritable modifications of the chromatin structure, which do not involve any alteration of the DNA sequence but nonetheless affect gene expression. These mechanisms play an important role in cell differentiation, but aberrant occurrences are also associated with a number of diseases, including cancer and neural development disorders. In particular, aberrant DNA methylation induced by H. Pylori has been found to be a significant risk factor in gastric cancer. To investigate the sensitivity of different genes and cell types to this infection, a computational model of methylation in gastric crypts is developed. In this article, we review existing results from physical experiments and outline their limitations, before presenting the computational model and investigating the influence of its parameters.

Physical performance and self-efficacy under happy and sad moods

Two experiments involving 87 undergraduates examined whether happiness produces increased performance on a physical task and tested whether self-efficacy mediated the results. When mood inductions covered the full range from happy to sad, mood influenced physical performance; however, evidence regarding self-efficacy was equivocal. Efficacy for the performed task was unaffected by mood, although it remained a good predictor of performance. Since mood altered efficacy for a nonperformed but more familiar task, inconsistent efficacy results could reflect task differences. Findings offer prospects for the use of mood inductions in practical sporting situations.

Physical characteristics of small ions and their interaction with ultrafine particles in the urban environment

In recent years, the effect of ions and ultrafine particles on ambient air quality and human health has been well documented, however, knowledge about their sources, concentrations and interactions within different types of urban environments remains limited. This thesis presents the results of numerous field studies aimed at quantifying variations in ion concentration with distance from the source, as well as identifying the dynamics of the particle ionisation processes which lead to the formation of charged particles in the air. In order to select the most appropriate measurement instruments and locations for the studies, a literature review was also conducted on studies that reported ion and ultrafine particle emissions from different sources in a typical urban environment. The initial study involved laboratory experiments on the attachment of ions to aerosols, so as to gain a better understanding of the interaction between ions and particles. This study determined the efficiency of corona ions at charging and removing particles from the air, as a function of different particle number and ion concentrations. The results showed that particle number loss was directly proportional to particle charge concentration, and that higher small ion concentrations led to higher particle deposition rates in all size ranges investigated. Nanoparticles were also observed to decrease with increasing particle charge concentration, due to their higher Brownian mobility and subsequent attachment to charged particles. Given that corona discharge from high voltage powerlines is considered one of the major ion sources in urban areas, a detailed study was then conducted under three parallel overhead powerlines, with a steady wind blowing in a perpendicular direction to the lines. The results showed that large sections of the lines did not produce any corona at all, while strong positive emissions were observed from discrete components such as a particular set of spacers on one of the lines. Measurements were also conducted at eight upwind and downwind points perpendicular to the powerlines, spanning a total distance of about 160m. The maximum positive small and large ion concentrations, and DC electric field were observed at a point 20 m downwind from the lines, with median values of 4.4×103 cm-3, 1.3×103 cm-3 and 530 V m-1, respectively. It was estimated that, at this point, less than 7% of the total number of particles was charged. The electrical parameters decreased steadily with increasing downwind distance from the lines but remained significantly higher than background levels at the limit of the measurements. Moreover, vehicles are one of the most prevalent ion and particle emitting sources in urban environments, and therefore, experiments were also conducted behind a motor vehicle exhaust pipe and near busy motorways, with the aim of quantifying small ion and particle charge concentration, as well as their distribution as a function of distance from the source. The study found that approximately equal numbers of positive and negative ions were observed in the vehicle exhaust plume, as well as near motorways, of which heavy duty vehicles were believed to be the main contributor. In addition, cluster ion concentration was observed to decrease rapidly within the first 10-15 m from the road and ion-ion recombination and ion-aerosol attachment were the most likely cause of ion depletion, rather than dilution and turbulence related processes. In addition to the above-mentioned dominant ion sources, other sources also exist within urban environments where intensive human activities take place. In this part of the study, airborne concentrations of small ions, particles and net particle charge were measured at 32 different outdoor sites in and around Brisbane, Australia, which were classified into seven different groups as follows: park, woodland, city centre, residential, freeway, powerlines and power substation. Whilst the study confirmed that powerlines, power substations and freeways were the main ion sources in an urban environment, it also suggested that not all powerlines emitted ions, only those with discrete corona discharge points. In addition to the main ion sources, higher ion concentrations were also observed environments affected by vehicle traffic and human activities, such as the city centre and residential areas. A considerable number of ions were also observed in a woodland area and it is still unclear if they were emitted directly from the trees, or if they originated from some other local source. Overall, it was found that different types of environments had different types of ion sources, which could be classified as unipolar or bipolar particle sources, as well as ion sources that co-exist with particle sources. In general, fewer small ions were observed at sites with co-existing sources, however particle charge was often higher due to the effect of ion-particle attachment. In summary, this study quantified ion concentrations in typical urban environments, identified major charge sources in urban areas, and determined the spatial dispersion of ions as a function of distance from the source, as well as their controlling factors. The study also presented ion-aerosol attachment efficiencies under high ion concentration conditions, both in the laboratory and in real outdoor environments. The outcomes of these studies addressed the aims of this work and advanced understanding of the charge status of aerosols in the urban environment.

Influence of physical and chemical properties of solids on heavy metal adsorption

Partition of heavy metals between particulate and dissolve fraction of stormwater primarily depends on the adsorption characteristics of solids particles. Moreover, the bioavailability of heavy metals is also influenced by the adsorption behaviour of solids. However, due to the lack of fundamental knowledge in relation to the heavy metals adsorption processes of road deposited solids, the effectiveness of stormwater management strategies can be limited. The research study focused on the investigation of the physical and chemical parameters of solids on urban road surfaces and, more specifically, on heavy metal adsorption to solids. Due to the complex nature of heavy metal interaction with solids, a substantial database was generated through a series of field investigations and laboratory experiments. The study sites for the build-up pollutant sample collection were selected from four urbanised suburbs located in a major river catchment. Sixteen road sites were selected from these suburbs and represented typical industrial, commercial and residential land uses. Build-up pollutants were collected using a wet and dry vacuum collection technique which was specially designed to improve fine particle collection. Roadside soil samples were also collected from each suburb for comparison with the road surface solids. The collected build-up solids samples were separated into four particle size ranges and tested for a range of physical and chemical parameters. The solids build-up on road surfaces contained a high fraction (70%) of particles smaller than 150ìm, which are favourable for heavy metal adsorption. These solids particles predominantly consist of soil derived minerals which included quartz, albite, microcline, muscovite and chlorite. Additionally, a high percentage of amorphous content was also identified in road deposited solids. In comparing the mineralogical data of surrounding soil and road deposited solids, it was found that about 30% of the solids consisted of particles generated from traffic related activities on road surfaces. Significant difference in mineralogical composition was noted in different particle sizes of build-up solids. Fine solids particles (<150ìm) consisted of a clayey matrix and high amorphous content (in the region of 40%) while coarse particles (>150ìm) consisted of a sandy matrix at all study sites, with about 60% quartz content. Due to these differences in mineralogical components, particles larger than and smaller than 150ìm had significant differences in their specific surface area (SSA) and effective cation exchange capacity (ECEC). These parameters, in turn, exert a significant influence on heavy metal adsorption. Consequently, heavy metal content in >150ìm particles was lower than in the case of fine particles. The particle size range <75ìm had the highest heavy metal content, corresponding with its high clay forming minerals, high organic matter and low quartz content which increased the SSA, ECEC and the presence of Fe, Al and Mn oxides. The clay forming minerals, high organic matter and Fe, Al and Mn oxides create distinct groups of charge sites on solids surfaces and exhibit different adsorption mechanisms and bond strength, between heavy metal elements and charge sites. Therefore, the predominance of these factors in different particle sizes leads to different heavy metal adsorption characteristics. Heavy metals show preference for association with clay forming minerals in fine solids particles, whilst in coarse particles heavy metals preferentially associate with organic matter. Although heavy metal adsorption to amorphous material is very low, the heavy metals embedded in traffic related materials have a potential impact on stormwater quality.Adsorption of heavy metals is not confined to an individual type of charge site in solids, whereas specific heavy metal elements show preference for adsorption to several different types of charge sites in solids. This is attributed to the dearth of preferred binding sites and the inability to reach the preferred binding sites due to competition between different heavy metal species. This confirms that heavy metal adsorption is significantly influenced by the physical and chemical parameters of solids that lead to a heterogeneity of surface charge sites. The research study highlighted the importance of removal of solids particles from stormwater runoff before they enter into receiving waters to reduce the potential risk posed by the bioavailability of heavy metals. The bioavailability of heavy metals not only results from the easily mobile fraction bound to the solids particles, but can also occur as a result of the dissolution of other forms of bonds by chemical changes in stormwater or microbial activity. Due to the diversity in the composition of the different particle sizes of solids and the characteristics and amount of charge sites on the particle surfaces, investigations using bulk solids are not adequate to gain an understanding of the heavy metal adsorption processes of solids particles. Therefore, the investigation of different particle size ranges is recommended for enhancing stormwater quality management practices.

Power-law viscous materials for analogue experiments: New data on the rheology of highly-filled silicone polymers

The selection of appropriate analogue materials is a central consideration in the design of realistic physical models. We investigate the rheology of highly-filled silicone polymers in order to find materials with a power-law strain-rate softening rheology suitable for modelling rock deformation by dislocation creep and report the rheological properties of the materials as functions of the filler content. The mixtures exhibit strain-rate softening behaviour but with increasing amounts of filler become strain-dependent. For the strain-independent viscous materials, flow laws are presented while for strain-dependent materials the relative importance of strain and strain rate softening/hardening is reported. If the stress or strain rate is above a threshold value some highly-filled silicone polymers may be considered linear visco-elastic (strain independent) and power-law strain-rate softening. The power-law exponent can be raised from 1 to ~3 by using mixtures of high-viscosity silicone and plasticine. However, the need for high shear strain rates to obtain the power-law rheology imposes some restrictions on the usage of such materials for geodynamic modelling. Two simple shear experiments are presented that use Newtonian and power-law strain-rate softening materials. The results demonstrate how materials with power-law rheology result in better strain localization in analogue experiments.

In vitro physical stimulation of tissue-engineered and native cartilage

Because of the limited availability of donor cartilage for resurfacing defects in articular surfaces, there is tremendous interest in the in vitro bioengineering of cartilage replacements for clinical applications. However, attaining mechanical properties in engineered cartilaginous constructs that approach those of native cartilage has not been previously achieved when constructs are cultured under free-swelling conditions. One approach toward stimulating the development of constructs that are mechanically more robust is to expose them to physical environments that are similar, in certain ways, to those encountered by native cartilage. This is a strategy motivated by observations in numerous short-term experiments that certain mechanical signals are potent stimulators of cartilage metabolism. On the other hand, excess mechanical loading can have a deleterious effect on cartilage. Culture conditions that include a physical stimulation component are made possible by the use of specialized bioreactors. This chapter addresses some of the issues involved in using bioreactors as integral components of cartilage tissue engineering and in studying the physical regulation of cartilage. We first consider the generation of cartilaginous constructs in vitro. Next we describe the rationale and design of bioreactors that can impart either mechanical deformation or fluid-induced mechanical signals.

Experiments with cooperative control of underwater robots

In this paper we describe cooperative control algorithms for robots and sensor nodes in an underwater environment. Cooperative navigation is defined as the ability of a coupled system of autonomous robots to pool their resources to achieve long-distance navigation and a larger controllability space. Other types of useful cooperation in underwater environments include: exchange of information such as data download and retasking; cooperative localization and tracking; and physical connection (docking) for tasks such as deployment of underwater sensor networks, collection of nodes and rescue of damaged robots. We present experimental results obtained with an underwater system that consists of two very different robots and a number of sensor network modules. We present the hardware and software architecture of this underwater system. We then describe various interactions between the robots and sensor nodes and between the two robots, including cooperative navigation. Finally, we describe our experiments with this underwater system and present data.

A Cyber-Physical System Simulator for risk-free transport studies

The article introduces a novel platform for conducting controlled and risk-free driving and traveling behavior studies, called Cyber-Physical System Simulator (CPSS). The key features of CPSS are: (1) simulation of multiuser immersive driving in a threedimensional (3D) virtual environment; (2) integration of traffic and communication simulators with human driving based on dedicated middleware; and (3) accessibility of multiuser driving simulator on popular software and hardware platforms. This combination of features allows us to easily collect large-scale data on interesting phenomena regarding the interaction between multiple user drivers, which is not possible with current single-user driving simulators. The core original contribution of this article is threefold: (1) we introduce a multiuser driving simulator based on DiVE, our original massively multiuser networked 3D virtual environment; (2) we introduce OpenV2X, a middleware for simulating vehicle-to-vehicle and vehicle to infrastructure communication; and (3) we present two experiments based on our CPSS platform. The first experiment investigates the “rubbernecking” phenomenon, where a platoon of four user drivers experiences an accident in the oncoming direction of traffic. Second, we report on a pilot study about the effectiveness of a Cooperative Intelligent Transport Systems advisory system.

Drying characteristics and quality of grape under physical pretreatment

Grape drying is a slow and energy intensive process because the waxy peel has low permeability to moisture. Therefore, peel chemical and physical pretreatments are considered before drying in order to facilitate water diffusion. However, they cause heterogeneity in the waxes removal and problems during shelf-life. In this paper an alternative abrasive pretreatment of grape peel, for enhancing the drying rate and preserving the samples, was applied to Red Globe grapes. Convective drying experiments were carried out at 40-70 Centigrade and at 2.3 m/s air velocity. The effect of wax abrasive pretreatment on the drying kinetics and quality parameters of raisins was investigated. The results were compared with those of samples pretreated by dipping in alkaline ethyl oleate solution and untreated grapes. All the dried samples are darker than fresh one and shrunked. The samples pretreated by peel abrasion and dried at 50 centigrade showed the lowest color changes, less shrinkage and the best rehydration capacity. The drying kinetics and shrinkage curves were also analyzed using some commonly available empirical models.