Can current force fields reproduce ring puckering in 2-O-sulfo-α-l-iduronic acid? A molecular dynamics simulation study

The monosaccharide 2-O-sulfo-α-l-iduronic acid (IdoA2S) is one of the major components of glycosaminoglycans. The ability of molecular mechanics force fields to reproduce ring-puckering conformational equilibrium is important for the successful prediction of the free energies of interaction of these carbohydrates with proteins. Here we report unconstrained molecular dynamics simulations of IdoA2S monosaccharide that were carried out to investigate the ability of commonly used force fields to reproduce its ring conformational flexibility in aqueous solution. In particular, the distribution of ring conformer populations of IdoA2S was determined. The GROMOS96 force field with the SPC/E water potential can predict successfully the dominant skew-boat to chair conformational transition of the IdoA2S monosaccharide in aqueous solution. On the other hand, the GLYCAM06 force field with the TIP3P water potential sampled transitional conformations between the boat and chair forms. Simulations using the GROMOS96 force field showed no pseudorotational equilibrium fluctuations and hence no inter-conversion between the boat and twist boat ring conformers. Calculations of theoretical proton NMR coupling constants showed that the GROMOS96 force field can predict the skew-boat to chair conformational ratio in good agreement with the experiment, whereas GLYCAM06 shows worse agreement. The omega rotamer distribution about the C5–C6 bond was predicted by both force fields to have torsions around 10°, 190°, and 360°.

Advanced mathematical modelling and experimental investigation of new torque arms for shaft-mounted drives

Shaft-mounted gearboxes are widely used in industry. The torque arm that holds the reactive torque on the housing of the gearbox, if properly positioned creates the reactive force that lifts the gearbox and unloads the bearings of the output shaft. The shortcoming of these torque arms is that if the gearbox is reversed the direction of the reactive force on the torque arm changes to opposite and added to the weight of the gearbox overloads the bearings shortening their operating life. In this paper, a new patented design of torque arms that develop a controlled lifting force and counteract the weight of the gearbox regardless of the direction of the output shaft rotation is described. Several mathematical models of the conventional and new torque arms were developed and verified experimentally on a specially built test rig that enables modelling of the radial compliance of the gearbox bearings and elastic elements of the torque arms. Comparison showed a good agreement between theoretical and experimental results.

The current context of Queensland primary teacher engagement with professional learning through professional associations

Engaging Queensland primary teachers in professional associations can be a challenge, particularly for subject-specific associations. Professional associations are recognised providers of professional learning. By not being involved in professional associations primary teachers are missing potential quality professional learning opportunities that can impact the results of their students. The purpose of the research is twofold: Firstly, to provide a thorough understanding of the current context in order to assist professional associations who wish to change from their current level of primary teacher engagement; and secondly, to contribute to the literature in the area of professional learning for primary teachers within professional associations. Using a three part research design, interviews of primary teachers and focus groups of professional association participants and executives were conducted and themed to examine the current context of engagement. Force field analysis was used to provide the framework to identify the driving and restraining forces for primary teacher engagement in professional learning through professional associations. Communities of practice and professional learning communities were specifically examined as potential models for professional associations to consider. The outcome is a diagrammatic framework outlining the current context of primary teacher engagement, specifically the driving and restraining forces of primary teacher engagement with professional associations. This research also identifies considerations for professional associations wishing to change their level of primary teacher engagement. The results of this research show that there are key themes that provide maximum impact if wishing to increase engagement of primary teachers in professional associations. However the implications of this lies with professional associations and their alignment between intent and practice dedicated to this change.

The implementation of a guideline of care for patients with a Sengstaken-Blakemore tube in situ in a general intensive care unit using transitional change theory

The use of the Sengstaken–Blakemore tube as a life-saving treatment for bleeding oesophageal varices is slowly becoming the least preferred method possibly due to the potential complications associated with its placement. Nursing practice pertaining to the care of this patient group appears ad hoc and reliant on local knowledge and experience as opposed to recognised evidence of best practice. Therefore, this paper focuses on the application of Lewin's transitional change theory used to introduce a change in nursing practice with the application of a guideline to enhance the care of patients with a Sengstaken–Blakemore tube in situ within a general intensive care unit. This method identified some of the complexities surrounding the change process including the driving and restraining forces that must be harnessed and minimised in order for the adoption of change to be successful.

Intercalation of dodecylamine into kaolinite and its layering structure investigated by molecular dynamics simulation

Dodecylamine was successfully intercalated into the layer space of kaolinite by utilizing the methanol treated kaolinite–dimethyl sulfoxide (DMSO) intercalation complex as an intermediate. The basal spacing of kaolinite, measured by X-ray diffraction (XRD), increased from 0.72 nm to 4.29 nm after the intercalation of dodecylamine. Also, the significant variation observed in the Fourier Transform Infrared Spectroscopy (FTIR) spectra of kaolinite when intercalated with dodecylamine verified the feasibility of intercalation of dodecylamine into kaolinite. Isothermal-isobaric (NPT) molecular dynamics simulation with the use of Dreiding force field was performed to probe into the layering behavior and structure of nanoconfined dodecylamine in the kaolinite gallery. The concentration profiles of the nitrogen atom, methyl group and methylene group of intercalated dodecylamine molecules in the direction perpendicular to the kaolinite basal surface indicated that the alkyl chains within the interlayer space of kaolinite exhibited an obvious layering structure. However, the unified bilayer, pseudo-trilayer, or paraffin-type arrangements of alkyl chains deduced based on their chain length combined with the measured basal spacing of organoclays were not found in this study. The alkyl chains aggregated to a mixture of ordered paraffin-type-like structure and disordered gauche conformation in the middle interlayer space of kaolinite, and some alkyl chains arranged in two bilayer structures, in which one was close to the silica tetrahedron surface, and the other was close to the alumina octahedron surface with their alkyl chains parallel to the kaolinite basal surface.

Practical path planning and obstacle avoidance for autonomous mowing

There is a need for systems which can autonomously perform coverage tasks on large outdoor areas. Unfortunately, the state-of-the-art is to use GPS based localization, which is not suitable for precise operations near trees and other obstructions. In this paper we present a robotic platform for autonomous coverage tasks. The system architecture integrates laser based localization and mapping using the Atlas Framework with Rapidly-Exploring Random Trees path planning and Virtual Force Field obstacle avoidance. We demonstrate the performance of the system in simulation as well as with real world experiments.

Generalized element load method for first- and second-order element solutions with element load effect

The finite element method in principle adaptively divides the continuous domain with complex geometry into discrete simple subdomain by using an approximate element function, and the continuous element loads are also converted into the nodal load by means of the traditional lumping and consistent load methods, which can standardise a plethora of element loads into a typical numerical procedure, but element load effect is restricted to the nodal solution. It in turn means the accurate continuous element solutions with the element load effects are merely restricted to element nodes discretely, and further limited to either displacement or force field depending on which type of approximate function is derived. On the other hand, the analytical stability functions can give the accurate continuous element solutions due to element loads. Unfortunately, the expressions of stability functions are very diverse and distinct when subjected to different element loads that deter the numerical routine for practical applications. To this end, this paper presents a displacement-based finite element function (generalised element load method) with a plethora of element load effects in the similar fashion that never be achieved by the stability function, as well as it can generate the continuous first- and second-order elastic displacement and force solutions along an element without loss of accuracy considerably as the analytical approach that never be achieved by neither the lumping nor consistent load methods. Hence, the salient and unique features of this paper (generalised element load method) embody its robustness, versatility and accuracy in continuous element solutions when subjected to the great diversity of transverse element loads.

The subordinated processes controlled by a family of subordinators and corresponding Fokker-Planck type equations

In this work, we consider subordinated processes controlled by a family of subordinators which consist of a power function of a time variable and a negative power function of an α-stable random variable. The effect of parameters in the subordinators on the subordinated process is discussed. By suitable variable substitutions and the Laplace transform technique, the corresponding fractional Fokker–Planck-type equations are derived. We also compute their mean square displacements in a free force field. By choosing suitable ranges of parameters, the resulting subordinated processes may be subdiffusive, normal diffusive or superdiffusive

Calculations of the free energy of interaction of the c-Fos−c-Jun coiled coil: Effects of the solvation model and the inclusion of polarization effects

The leucine zipper region of activator protein-1 (AP-1) comprises the c-Jun and c-Fos proteins and constitutes a well-known coiled coil protein−protein interaction motif. We have used molecular dynamics (MD) simulations in conjunction with the molecular mechanics/Poisson−Boltzmann generalized-Born surface area [MM/PB(GB)SA] methods to predict the free energy of interaction of these proteins. In particular, the influence of the choice of solvation model, protein force field, and water potential on the stability and dynamic properties of the c-Fos−c-Jun complex were investigated. Use of the AMBER polarizable force field ff02 in combination with the polarizable POL3 water potential was found to result in increased stability of the c-Fos−c-Jun complex. MM/PB(GB)SA calculations revealed that MD simulations using the POL3 water potential give the lowest predicted free energies of interaction compared to other nonpolarizable water potentials. In addition, the calculated absolute free energy of binding was predicted to be closest to the experimental value using the MM/GBSA method with independent MD simulation trajectories using the POL3 water potential and the polarizable ff02 force field, while all other binding affinities were overestimated.

Field instrumentation of a water reticulation pipe buried in reactive soil

The loss of valuable water resources due to pipe failure has become a major problem in Australia, especially in areas under high level of water restrictions. Generally pipe failure occurs due to a combination of physical and environmental factors. Stresses induced by shrinking and swelling of reactive soils are one of the major factors affecting the performance of buried pipes. This paper presents the details of a field instrumentation undertaken to monitor the performance of an in-service water reticulation pipe buried in a reactive soil and subjected to seasonal climatic changes.

Symmetry of in-shoe force signatures in athletes under field conditions : an application for injury prevention

The aetiology behind overuse injuries such as stress fractures is complex and multi-factorial. In sporting events where the loading is likely to be uneven (e.g. hurdling and jumps), research has suggested that the frequency of stress fractures seems to favour the athlete’s dominant limb. The tendency for an individual to have a preferred limb for voluntary motor acts makes limb selection a possible factor behind the development of unilateral overuse injuries, particularly when repeatedly used during high loading activities. The event of sprint hurdling is well suited for the study of loading asymmetry as the hurdling technique is repetitive and the limb movement asymmetrical. Of relevance to this study is the high incidence of Navicular Stress Fractures (NSF) in hurdlers, with suggestions there is a tendency for the fracture to develop in the trail leg foot, although this is not fully accepted. The Ground Reaction Force (GRF) with each foot contact is influenced by the hurdle action, with research finding step-to-step loading variations. However, it is unknown if this loading asymmetry extends to individual forefoot joints, thereby influencing stress fracture development. The first part of the study involved a series of investigations using a commercially available matrix style in-shoe sensor system (FscanTM, Tekscan Inc.). The suitability of insole sensor systems and custom made discrete sensors for use in hurdling-related training activities was assessed. The methodology used to analyse foot loading with each technology was investigated. The insole and discrete sensors systems tested proved to be unsuitable for use during full pace hurdling. Instead, a running barrier task designed to replicate the four repetitive foot contacts present during hurdling was assessed. This involved the clearance of a series of 6 barriers (low training hurdles), place in a straight line, using 4 strides between each. The second part of the study involved the analysis of "inter-limb" and "within foot loading asymmetries" using stance duration as well as vertical GRF under the Hallux (T1), the first metatarsal head (M1) and the central forefoot peak pressure site (M2), during walking, running, and running with barrier clearances. The contribution to loading asymmetry that each of the four repetitive foot contacts made during a series of barrier clearances was also assessed. Inter-limb asymmetry, in forefoot loading, occurred at discrete forefoot sites in a non-uniform manner across the three gait conditions. When the individual barrier foot contacts were compared, the stance duration was asymmetrical and the proportion of total forefoot load at M2 was asymmetrical. There were no significant differences between the proportion of forefoot load at M1, compared to M2; for any of the steps involved in the barrier clearance. A case study testing experimental (discrete) sensors during full pace sprinting and hurdling found that during both gait conditions, the trail limb experienced the greater vertical GRF at M1 and M2. During full pace hurdling, increased stance duration and vertical loading was a characteristic of the trail limb hurdle foot contacts. Commercially available in-shoe systems are not suitable for on field assessment of full pace hurdling. For the use of discrete sensor technology to become commonplace in the field, more robust sensors need to be developed.

Field measurement of wheel-rail impact force at insulated rail joint

When wheels pass over insulated rail joints (IRJs) a vertical impact force is generated. The ability to measure the impact force is valuable as the force signature helps understand the behaviour of the IRJs, in particular their potential for failure. The impact forces are thought to be one of the main factors that cause damage to the IRJ and track components. Study of the deterioration mechanism helps finding new methods to improve the service life of IRJs in track. In this research, the strain-gage-based wheel load detector, for the first time, is employed to measure the wheel–rail contact-impact force at an IRJ in a heavy haul rail line. In this technique, the strain gages are installed within the IRJ assembly without disturbing the structural integrity of IRJ and arranged in a full wheatstone bridge to form a wheel load detector. The instrumented IRJ is first tested and calibrated in the lab and then installed in the field. For comparison purposes, a reference rail section is also instrumented with the same strain gage pattern as the IRJ. In this paper the measurement technique, the process of instrumentation, and tests as well as some typical data obtained from the field and the inferences are presented.

Field performance of in-service cast iron water reticulation pipe buried in reactive clay

Field monitoring is an important means for understanding soil behaviour and its interaction with buried structures such as pipeline. This paper details the successful instrumentation of a section of an in-service cast iron water main buried in an area of reactive clay where frequent water pipe breakage has been observed. The instrumentation included measurement of pipe strain; pipe water pressure and temperature; soil pressure, temperature, moisture content and matric suction, as well as the meteorological conditions on site. The data generally indicated that changes in soil temperature, suction and moisture content were directly related to the local climatic variations. The suction and moisture content data indicated that the soil profile at the site down to around 700 mm, and probably down to 1000 mm, is affected by changes in surface weather, while soil conditions below this depth appear to be more stable. Analysis of pipe strain indicated that the pipe behaves like a cantilever beam, with the top experiencing predominantly tensile strains during summer. Subsequently, these trends reduce to compressive strains as soil swelling occurs due to increase of moisture content with the onset of winter.

Field performance of in-service cast iron gas reticulation pipe buried in reactive clay

Field instrumentation of an in-service cast iron gas pipe buried in a residential area is detailed in this paper. The aim of the study was to monitor the long-term pipe behavior to understand the mechanisms of pipe bending in relation to ground movement as a result of seasonal fluctuation of soil moisture content. Field data showed that variation of soil temperature, suction, and moisture content are closely related to the prevailing climate. Change of soil temperature is generally related to the ambient air temperature, with a variation of approximately −3°C −3°C per meter depth from the ground surface in summer (decrease with depth) and winter (increase with depth). Seasonal cyclic variation in moisture content was observed with maxima in February and March, and a minimum around September. The pipe top was under tensile strain during summer and subsequently subjected to compressive strain as soil swelling occurred as a result of increase in moisture content. The study suggests that downward pipe bending occurs in summer because of soil shrinkage, while upward pipe bending occurs in winter when the soil swells.

Flow field investigation in a water treatment reactor using computational fluid dynamics

The hydrodynamic behaviour of a novel flat plate photocatalytic reactor for water treatment is investigated using CFD code FLUENT. The reactor consists of a reactive section that features negligible pressure drop and uniform illumination of the photocatalyst to ensure enhanced photocatalytic efficiency. The numerical simulations allowed the identification of several design issues in the original reactor, which include extensive boundary layer separation near the photocatalyst support and regions of flow recirculation that render a significant portion of the reactive area. The simulations reveal that this issue could be addressed by selecting the appropriate inlet positions and configurations. This modification can cause minimal pressure drop across the reactive zone and achieves significant uniformization of the tested pollutant on the photocatalyst surface. The influence of roughness elements type has also been studied with a view to identify their role on the distribution of pollutant concentration on the photocatalyst surface. The results presented here indicate that the flow and pollutant concentration field strongly depend on the geometric parameters and flow conditions.