Digital Commons Network^™

Pepblock Builder Vr – An Open-Source Tool For Gaming-Based Bio-Edutainment In Interactive Protein Design, Venkata V. B. Yallapragada, Tianshu Xu, Sidney P. Walker, Sabin Tabirca, Mark Tangney

Cappa Publications

Proteins mediate and perform various fundamental functions of life. This versatility of protein function is an attribute of its 3D structure. In recent years, our understanding of protein 3D structure has been complemented with advances in computational and mathematical tools for protein modelling and protein design. 3D molecular visualisation is an essential part in every protein design and protein modelling workflow. Over the years, stand-alone and web-based molecular visualisation tools have been used to emulate three-dimensional view on computers. The advent of virtual reality provided the scope for immersive control of molecular visualisation. While these technologies have significantly improved our …

Fredholm-Regularity Of Holomorphic Discs In Plane Bundles Over Compact Surfaces, Brendan Guilfoyle, Wilhelm Klingenberg

Publications

We study the space of holomorphic discs with boundary on a surface in a real 2-dimensional vector bundle over a compact 2-manifold. We prove that, if the ambient 4-manifold admits a fibre-preserving transitive holomorphic action, then a section with a single complex point has C2,α-close sections such that any (non-multiply covered) holomorphic disc with boundary in these sections are Fredholm regular. Fredholm regularity is also established when the complex surface is neutral K¨ahler, the action is both holomorphic and symplectic, and the section is Lagrangian with a single complex point.

Influences Of Catchment And River Channel Characteristics On The Magnitude And Dynamics Of Storage And Re-Suspension Of Fine Sediments In River Beds, Jungsu Park, Ramon J. Batalla, François Bírgand, Michel Esteves, Francesco Gentile, Joseph R. Harrington, Oldrich Navratil, José Andres López-Tarazón, Damiá Vericant

Publications

Fine particles or sediments are one of the important variables that should be considered for the proper management of water quality and aquatic ecosystems. In the present study, the effect of catchment characteristics on the performance of an already developed model for the estimation of fine sediments dynamics between the water column and sediment bed was tested, using 13 catchments distributed worldwide. The model was calibrated to determine two optimal model parameters. The first is the filtration parameter, which represents the filtration of fine sediments through pores of the stream bed during the recession period of a flood event. The …

Mid-Infrared Optical Sensing Using Sub-Wavelength Gratings, Brian Hogan, Liam Lewis, Michael Mcauliffe, Stephen P. Hegarty

Cappa Publications

Optical sensing has shown great potential for both quantitative and qualitative analysis of compounds. In particular sensors which are capable of detecting changes in refractive index at a surface as well as in bulk material have received much attention. Much of the recent research has focused on developing technologies that enable such sensors to be deployed in an integrated photonic device. In this work we demonstrate experimentally, using a sub-wavelength grating the detection of ethanol in aqueous solution by interrogating its large absorption band at 9.54 µm. Theoretical investigation of the operating principle of our grating sensor shows that in …

Mean Curvature Flow Of Compact Spacelike Submanifolds In Higher Codimension, Brendan Guilfoyle, Wilhelm Klingenberg

Publications

We prove long-time existence for mean curvature flow of a smooth n-dimensional spacelike submanifold of an n + m dimensional manifold whose metric satisfies the timelike curvature condition.

A Global Version Of A Classical Result Of Joachimstha, Brendan Guilfoyle, Wilhelm Klingenberg

Publications

A classical result attributed to Joachimsthal in 1846 states that if two surfaces intersect with constant angle along a line of curvature of one surface, then the curve of intersection is also a line of curvature of the other surface. In this note we prove the following global analogue of this result. Suppose that two closed convex surfaces intersect with constant angle along a curve that is not umbilic in either surface. We prove that the principal foliations of the two surfaces along the curve are either both orientable, or both nonorientable. We prove this by characterizing the constant angle …

Mitigating The Structural Vibrations Of Wind Turbines Using Tuned Liquid Column Damper Considering Soil-Structure Interaction, Tadhg Buckley, Phoebe Watson, Paul Cahill, Vesna Jaksic, Vikram Pakrashi

Publications

This paper considers the potential of using a Tuned Liquid Column Damper (TLCD) to reduce structural vibrations of a wind turbine tower. The effect of TLCD on wind turbine towers, including the soil-structure interactions for a monopile foundation was modelled theoretically and scaled laboratory experiments were carried out to validate these results. The tower of the turbine is represented as a Euler beam with a set of springs at the boundary to simulate the soil-structure interaction. TLCD design was carried out using such a model and the reduction in tower vibrations due to the deployment of TLCD was then examined …

A Decision Support Tool For Building Integrated Renewable Energy Microgrids Connected To A Smart Grid, Damilola A. Asaleye, Michael D. Murphy, Michael Breen

Publications

The objective of this study was to create a tool that will enable renewable energy microgrid (REμG) facility users to make informed decisions on the utilization of electrical power output from a building integrated REμG connected to a smart grid. A decision support tool for renewable energy microgrids (DSTREM) capable of predicting photovoltaic array and wind turbine power outputs was developed. The tool simulated users’ daily electricity consumption costs, avoided CO₂ emissions and incurred monetary income relative to the usage of the building integrated REμG connected to the national electricity smart grid. DSTREM forecasted climate variables, which were used …

Parabolic Classical Curvature Flows, Brendan Guilfoyle, Wilhelm Klingenberg

Publications

We consider classical curvature flows: 1-parameter families of convex embeddings of the 2-sphere into Euclidean 3-space, which evolve by an arbitrary (nonhomogeneous) function of the radii of curvature (RoC). We determine conditions for parabolic flows that ensure the boundedness of various geometric quantities and investigate some examples. As a new tool, we introduce the RoC diagram of a surface and its hyperbolic or anti-de Sitter metric. The relationship between the RoC diagram and the properties of Weingarten surfaces is also discussed.

Hopf Hypersurfaces In Spaces Of Oriented Geodesics., Nikos Georgiou, Brendan Guilfoyle

Publications

A Hopf hypersurface in a (para-)Kaehler manifold is a real hypersurface for which one of the principal directions of the second fundamental form is the (para-)complex dual of the normal vector. We consider particular Hopf hypersurfaces in the space of oriented geodesics of a non-flat space form of dimension greater than 2. For spherical and hyperbolic space forms, the space of oriented geodesics admits a canonical Kaehler–Einstein and para-Kaehler–Einstein structure, respectively, so that a natural notion of a Hopf hypersurface exists. The particular hypersurfaces considered are formed by the oriented geodesics that are tangent to a given convex hypersurface in …

A Converging Lagrangian Flow In The Space Of Oriented Lines, Brendan Guilfoyle, Wilhelm Klingenberg

Publications

Under mean radius of curvature flow, a closed convex surface in Euclidean space is known to expand exponentially to infinity. In the three-dimensional case we prove that the oriented normals to the flowing surface converge to the oriented normals of a round sphere whose centre is the Steiner point of the initial surface, which remains constant under the flow.
To prove this we show that the oriented normal lines, considered as a surface in the space of all oriented lines, evolve by a parabolic flow which preserves the Lagrangian condition.Moreover, this flow converges to a holomorphic Lagrangian section, which forms …

Economic Modelling Of The Management Of Dredged Marine Sediments, Joseph R. Harrington, Jimmy Murphy, Mary Coleman, Declan Jordan, Tristan Debuigne, Gabor Szacsuri

Publications

This paper presents and applies an economic model developed for the management of dredged marine sediments. The model predicts direct project costs and direct, indirect and induced economic impacts. The model is applied to analyse the economic aspect of the specific potential beneficial use of dredged sediment for land rec-lamation in an Irish context. The model results show the potential economic benefits to land reclamation of using dredged sediment including its value as a potential substitute for quarry based material and as an alternative to traditional offshore dredged sediment disposal, where appropriate. Analysis of other sediment management ap-proaches including wetland …

Totally Null Surfaces In Neutral K¨Ahler 4-Manifolds, Nikos Georgiou, Brendan Guilfoyle, Wilhelm Klingenberg

Publications

We study the totally null surfaces of the neutral K¨ahler metric on certain 4-manifolds. The tangent spaces of totally null surfaces are either self-dual (α-planes) or anti-self-dual (β-planes) and so we consider α-surfaces and β-surfaces. The metric of the examples we study, which include the spaces of oriented geodesics of 3-manifolds of constant curvature, are anti-self-dual, and so it is well-known that the α-planes are integrable and α-surfaces exist. These are holomorphic Lagrangian surfaces, which for the geodesic spaces correspond to totally umbilic foliations of the underlying 3-manifold. The β-surfaces are less known and our interest is mainly in their …

The Definitions Of Three-Dimensional Landmarks On The Human Face: An Interdisciplinary View, Stanislav Katina, Kathryn Mcneil, Ashraf Ayoub, Brendan Guilfoyle, Balvinder Khambay, Paul Siebert, Federico Sukno, Mario Rojas, Liberty Vittert, John Waddington, Paul F. Whelan, Adrian W. Bowman

Publications

The analysis of shape is a key part of anatomical research and in the large majority of cases landmarks provide a standard starting point. However, while the technology of image capture has developed rapidly and in particular three-dimensional imaging is widely available, the definitions of anatomical landmarks remain rooted in their two-dimensional origins. In the important case of the human face, standard definitions often require careful orientation of the subject. This paper considers the definitions of facial landmarks from an interdisciplinary perspective, including biological and clinical motivations, issues associated with imaging and subsequent analysis, and the mathematical definition of surface …

Dynamics Of Suspended Sediment Flux On The Rivers Bandon And Owenabue, Ireland, S. T. Harrington, Joseph R. Harrington

Publications

Monitoring, analysis and modelling of suspended sediment transport in riverine systems has received much attention in recent decades. Quantitive analysis techniques have been applied to allow river basin managers to assess suspended sediment transport and its importance in transporting a range of pollutants including excess metals and nutrients, which negatively impact on aquatic systems. In this paper, an analysis of the suspended sediment fl ux (SSF) dynamics is presented for the small and medium sized catchments of the River Owenabue and the River Bandon, respectively. The results contribute to the fi lling of a research gap in an Irish context …

Dissolved And Particulate Nutrient Transport Dynamics Of A Small Irish Catchment: The River Owenabue, S. T. Harrington, Joseph R. Harrington

Publications

The objective of this research was to investigate the relationship between water and sediment discharge on the transport of nutrients: nitrogen and phosphorus. Water discharge, suspended sediment concentration and dissolved and particulate forms of nitrogen and phosphorus were monitored on the 105 km2 River Owenabue catchment in Ireland. Water discharge was found to have an influence on both particulate and dissolved nutrient transport, but more so for particulate nutrients. The particulate portion of N and P in collected samples was found to be 24 and 39 %, respectively. Increased particulate nitrogen concentrations were found at the onset of high discharge …

Stock Aggregation Model And Virtual Archetype For Large Scale Retrofit Modelling Of Local Authority Housing In Ireland, James Pittam, Paul D. O’Sullivan, Garrett O’Sullivan

Conference Papers

Developing representative archetypes using a bottom up approach for stock modelling is an excellent tool for evaluating the overall performance of the building stock; however it requires detailed analysis of the various building types. Currently there is no detailed housing data base for Local Authority housing in Cork City, Ireland that catalogues the housing stocks geometric properties and thermal characteristics for each typology. This study details a methodology to catalogue the LAH stock and build a detailed housing data base. The GIS web based mapping application Google Street View is used to identify 20 house typologies across 36 LAH developments; …

A Modified Surface On Titanium Deposited By A Blasting Process, Caroline O' Sullivan, Peter O'Hare, Greg Byrne, Liam O'Neill, Katie B. Ryan, Abina M. Crean

Publications

Abstract

: Hydroxyapatite (HA) coating of hard tissue implants is widely employed for its biocompatible and osteoconductive properties as well as its improved mechanical properties. Plasma technology is the principal deposition process for coating HA on bioactive metals for this application. However, thermal decomposition of HA can occur during the plasma deposition process, resulting in coating variability in terms of purity, uniformity and crystallinity, which can lead to implant failure caused by aseptic loosening. In this study, CoBlast™, a novel blasting process has been used to successfully modify a titanium (V) substrate with a HA treatment using a dopant/abrasive regime. …

On The Geometry Of Spaces Of Oriented Geodesics., Dmitri V. Alekseevsky, Brendan Guilfoyle, Wilhelm Klingenberg

Publications

Let M be either a simply connected pseudo-Riemannian space of constant curvature or a rank one Riemannian symmetric space other than OH2 , and consider the space L(M) of oriented geodesics of M. The space L(M) is a smooth homogeneous manifold and in this paper we describe all invariant symplectic structures, (para)complex structures, pseudo-Riemannian metrics and (para)K¨ahler structure on L(M).

On The Three-Dimensional Blaschke-Lebesgue Problem, Henri Anciaux, Brendan Guilfoyle

Publications

The width of a closed convex subset of n-dimensional Euclidean space is the distance between two parallel supporting hyperplanes. The Blaschke-Lebesgue problem consists of minimizing the volume in the class of convex sets of fixed constant width and is still open in dimension n ≥ 3. In this paper we describe a necessary condition that the minimizer of the Blaschke-Lebesgue must satisfy in dimension n = 3: we prove that the smooth components of the boundary of the minimizer have their smaller principal curvature constant and therefore are either spherical caps or pieces of tubes (canal surfaces).

Lagrangian Curves On Spectral Curves Of Monopoles, Brendan Guilfoyle, Madeeha Khalid, Jose J. Ramon Marı

Publications

We study Lagrangian points on smooth holomorphic curves in TP 1 equipped with a natural neutral K¨ahler structure, and prove that they must form real curves. By virtue of the identification of TP 1 with the space L(E 3 ) of oriented affine lines in Euclidean 3-space E 3 , these Lagrangian curves give rise to ruled surfaces in E 3 , which we prove have zero Gauss curvature. Each ruled surface is shown to be the tangent lines to a curve in E 3 , called the edge of regression of the ruled surface. We give an alternative characterization …

Dredging And Dredged Material Beneficial Use In Ireland, Colm Sheehan, Joseph R. Harrington, Jerry Murphy

Publications

This article provides an overview of the dredging industry in Ireland which may be small by international standards but is of critical importance to the nation’s Ports and Harbours. Open sea disposal of dredged material is most common, but a range of beneficial uses for the coarser fraction of dredged material has been practiced. Details on different aspects of dredging in Ireland are presented including a review of current beneficial uses. A specific site at Fenit Harbour in Tralee Bay is examined to assess the potential for a specific beneficial use of dredged material using geotubes in breakwater and revetment …