School of Mathematics, Statistics and Applied Mathematics
Seventh Annual Research Day
21 April 2016
Programme
9.15-9.30
9.30-9.45
9.45-10.30
10.30-11.00
11.00-11.30
11.30-12.00
Lectures take place in AC201
Coffee, lunch, posters and reception take place in the Orbsen Building Atrium
Dr Ray Ryan
Welcome by the Head of School
Prof Lokesh Joshi
Welcome by the Vice-President for Research
Prof Werner Nahm FRS (Dublin IAS)
Title: Quantum fields and automorphic forms
Abstract: Quantum fields are among the most essential tools for modern physics, but have
not made it into the toolkit of mathematicians yet. The talk will show how mathematicians
can handle them. As an example the construction of automorphic forms for the mapping
class group of Riemann surfaces will be described, starting with tori and modular forms.
Coffee (Orbsen Building)
Dr Marianne Leitner (NUIG)
Title: Graphene and Grothendieck
Abstract: The quantum Hall effect is one of the most spectacular features of solid state
physics. It has a nice description in terms of Chern classes and the slope of vector bundles, a
dominant theme of 20th century mathematics. Graphene displays a peculiar quantum Hall
effect which seems to demand new mathematical structures.
Dr Jim Cruickshank (NUIG)
Title: Geometric Rigidity Theory
Abstract: Consider a collection of objects that are joined together by hinges. Is the
resulting structure rigid? This is the basic question at the heart of geometric rigidity theory.
There is a growing literature that considers various types of objects, hinges and notions of
rigidity. The theory draws on real algebraic geometry, graph theory, matroid theory and
linear algebra. It is also notable for its diverse domains of application - from protein flexibility
to structural engineering to modern art. I will present a brief survey of some of the highlights
of the mathematical theory and mention some problems that remain open.
(continued overleaf)
12.00-12.30
12.30-14.00
14.00-14.45
14.45-15.30
Cara Dooley (NUIG)
Title: Analysing Observational Studies
Abstract: Randomised control trials, where the experimenter allocates each
individual at random to the treatment or control group, are considered the
gold-standard for design of studies interested in estimating treatment effects.
However, there are many situations where we cannot allocate treatment at random, for example, for ethical or cost reasons. In these situations we carry out
an observational study. To properly analyse an observational study, thought
needs to be given to both the design and analysis of the data. Using tools including propensity scores and matching we can create a quasi-randomised trial
and remove bias from the estimate of the treatment effect.
Lunch
Prof Giuseppe Saccomandi (Universita di Perugia & NUIG)
Title: On the Equations Governing Nonlinear Symmetric Kirchhoff’s Elastic
Rods
Abstract: A systematic study of the equations governing nonlinear geometric
Kirchhoff’s Elastic Rods is provided. We discuss the integrability of the general
case and we investigate some special solutions. In particular we characterise
all the possible solutions that are Lancret’s helices.
Research blitz (Organizer: Dr Rachel Quinlan)
Short research talks by:
• Michel Destrade, Oblique Wrinkles
• Ronan Egan, A Brief Introduction to Error-Correcting Codes
• Olga O’Mahony, Minimal Graphs of Exponent 2
• James O’Shea, Homogeneous Polynomials of Degree 2
• Götz Pfeiffer, The Sections Lattice of the Klein 4-Group
• James Ward, A Lowbrow Limit
• Giuseppe Zurlo, Designing the Stress
15.30-17.00
16:00-17.00
Poster session (Orbsen Building)
Reception & poster prizes (Orbsen Building)
Research Day 2016: Introduction
1
1
Introduction
Welcome to the annual Research Day of the School of Mathematics, Statistics and Applied Mathematics. We
are delighted to welcome as our guest speakers this year Professor Giuseppe Saccomandi from Universita de
Perugia (who is also an Adjunct Professor in the School) and Professor Werner Nahm FRS, from the Dublin
Institute for Advanced Studies.
The research activity in the School is driven by our three research clusters:
• The De Brún Centre for Mathematics supports mathematical research across a spectrum of areas,
including Algebra, Analysis, Geometry, Topology and Mathematics Education.
• The Biostatistics/Bioinformatics Cluster covers the areas of Biostatistics and Bioinformatics and is
engaged in collaborative work with researchers in Genomics and other areas, and with clinicians, through
the Clinical Research Facility (CRF).
• The Stokes Applied Mathematics Cluster applies advanced mathematical skills to the modelling
of computational, physical and biological phenomena, with the aim of fostering interdisciplinary research
across the NUI Galway campus and beyond.
Some highlights from the year:
• We were delighted to welcome two new postdoctoral research fellows: Idemauro Rodrigues de Lara (working with John Hinde) and Arkady Zgonnikov (working with Petri Piiroinen, and with Denis O’Hora in
Psychology).
• We have been very fortunate in continuing to attract high quality PhD students and 2015 was no exception, with nine new research students joining us. The School won four IRC Postgraduate Scholarships,
surpassing all other schools. Our vibrant graduate school includes students from as far afield as Iran,
China, Vietnam, Argentina, Libya, Iraq and Brazil along with students from all parts of Ireland.
• We welcomed four new members to the School: Pilib O Broin (Bioinformatics), Cara Dooley (Statistics),
Marianne Leitner (Mathematics) and James O’Shea (Mathematics).
• Two new researchers joined the School as adjunct members: Giuseppe Saccomandi from Universita de
Perugia (Adjunct Professor in Applied Mathematics) and Alexander Rahm from Universite de Luxembourg
(Adjunct Lecturer in Mathematics).
• We were placed third in the whole of Ireland in the QS Subject Rankings.
• The School hosted four conferences:
– The 30th Summer Conference on Topology and Its Applications, funded by SFI.
– The Workshop on Vertex Operator Algebras, with funding from SFI and IRC.
– Groups in Galway, supported by the Irish Mathematical Society. This renowned conference has been
running annually since 1978.
– The second annual NUI Galway SIAM Student Chapter Conference.
• Members of the School published over 100 papers and gave over 50 invited lectures at international
institutions and conferences.
Ray Ryan,
Head of School
Research Day 2016: Posters
2
Poster Session
Mapper Algorithm and Groupoid
Methods for Data Analysis
Nisreen Alokbi
Supervisors: Graham Ellis
Topological methods are powerful tools for the analysis of high-dimensional data sets. One of these methods is the Mapper algorithm which can be used to
reduce high dimensional cloud data to a simplicial
complex. The fundamental groupoid of the simplicial
complex should enable one to access subtle homotopical invariants of cellular spaces arising in application
of topology.
The aim of the project is to design and implement algorithms that input large finite sets S of experimental
data from an unknown manifold M and, using unsupervised learning, attempt to return homotopical
invariants of M based on the fundamental groupoid.
[1] G. Singh, F. Mmoli, G. Carlsson. Topological
Methods for the Analysis of High Dimensional
Data Sets and 3D Object Recognition. Eurographics Symposium on Point-Based Graphics,
pp. 91-100, 2007.
[2] P. Higgins. Presentations of groupoids, with applications to groups. Cambridge Philosophical
Society, Mathematical Proceedings of the Cambridge Philosophical Society Volume 60, Issue
01, 7-20, 1994.
[3] R. Brown. Topology and groupoids. Printed by
Booksurge LLC, Charleston, S. Carolina, third
edition, 2006.
Cohomology Operations Of Finite
Groups
Daher Al Baydli
Supervisors: Prof. Graham Ellis, Dr.Emil
Skoeldberg
The main goal of the project is to develop algorithms
and software that can be used by mathematicians who
wish to investigate the standard cohomology operations (cup products, Bockstein operation, Steenrod
squares, Stiefel-Whitney classes of a real representation, Chern classes of a complex representation,...) in
the cohomology groups.
[1] Hatcher, Allen. Algebraic topology, Cambridge
University Press. New York, NY, USA, 2010.
2
[2] Graham,
Ellis.
An
introduction
to
Computational
Homotopy,
National University of Ireland,
Galway.
(http://hamilton.nuigalway.ie/, 2015
[3] Brown,
Kenneth
S.
Groups,Springer,1994.
Cohomology
of
Robust Solution of a Fourth-order
Singularly Perturbed Differential
Equation
Faiza Alssaedi
Supervisor: Niall Madden
We consider the numerical solution of a singularly
perturbed fourth-order differential equation by a finite difference method. Our study is motivation by a
problem that arises in the study of wave-current interactions [2]. The differential equation in question,
a variant on the Orr-Sommerfeld equation of hydrodynamic stability (see, e.g., [1]) is a complex-valued,
parameterised problem, with mixed boundary conditions. Moreover, the solution and its derivatives
possess boundary layers.
The goal of this presentation is to show that classical
methods are not suitable for solving this problem, and
to outline the basis for a successful strategy based
on the application of a finite difference scheme on a
specially designed non-uniform mesh [3].
References
[1] P. G. Drazin and W. H. Reid. Hydrodynamic stability. Cambridge University Press, 2nd edition,
2004.
[2] N. Madden, M. Stynes, and G.P. Thomas. On
the application of robust numerical methods to
a complete-flow wave-current model. In Proc.
BAIL, Toulouse, 2004.
[3] J. J. H. Miller, E. O’Riordan, and G. I. Shishkin.
Fitted numerical methods for singular perturbation problems. World Scientific Publishing Co.
Pte. Ltd., Hackensack, NJ, revised edition, 2012.
The universal Gröbner basis of a
binomial edge ideal
Isaac Burke
Supervisor: Dr Emil Sköldberg
Research Day 2016: Posters
We describe the universal Gröbner basis of a binomial edge ideal. We conjecture a similar result for a
parity binomial edge ideal and prove this conjecture
for the case when the underlying graph is the complete graph. The statistical background to this research problem is briefly explained and we also mention possibilities for further work. This is joint work
with Mourtadha Badiane and Emil Sköldberg.
[1] Jürgen Herzog, Takayuki Hibi, Freyja Hreinsdottir, and Thomas Kahle, Binomial edge ideals
and conditional independence statements, Advances in Applied Mathematics 45 (2010), no.
3, 317â 333.
[2] Thomas Kahle, Camilo Sarmiento, and Tobias Windisch, Parity binomial edge ideals, appeared online, Journal of Algebraic Combinatorics (2015), 1â 19.
[3] Mourtadha Badiane, Isaac Burke, and Emil
Sköldberg, The universal Gröbner basis of a binomial edge ideal, arXiv:1601.04575, submitted.
Supported by the Irish Research Council and the NUI Galway
Hardiman Scholarship Scheme.
Consensus of dynamic multi-agent
systems
Richard Burke
Supervisor: Petri T. Piiroinen
My research project is a study of dynamic multi-agent
systems in the context of evolving networks. Decentralised adaptive controls are utilised to feed information about the respecive agents’ states and communication lines between them to drive the larger group
from initial configurations of disarray toward more
desirable states of order. In particular we wish to effect a consensus in the network and investigate qualitative approximations of the consensus dynamics that
reduce the order of our systems but track essential
features such as the speed and profile of the larger
system’s convergence.
[1] Y. Cao, W. Yu, w. Ren and G. Chen, “An
overview of recent progress in the study of
distributed multi-agent coordination”, IEEE
Transactions on industrial informatics, vol. 9,
no. 1 (2013) pp. 427 438.
[2] R. Olfati-Saber and R. M. Murray, “Consensus
problems in networks of agents with switching
topology and time-delays”, IEEE Transactions
on automatic control, vol. 49, no. 9 (2004)
pp. 1520-1533.
3
[3] J. Yau, Z.H. Guan and D.J. Hill, “Passivitybased control and synchronization of general
complex dynamical networks”, Automatica,
vol.45, no. 9 (2009) pp. 2107-2113.
Genome assembly and characterisation
of Leishmania species
Simone Coughlan
Supervisors: Tim Downing, Cathal Seoighe
Effective molecular tools for monitoring the emergence of novel pathogens in domestic and peridomestic reservoir hosts are urgently required. Taxonomically classifying unknown samples of ambiguous origin and identifying optimal protocols for their genome
assembly using short-read data is required for comparison with known species. DNA was sampled from
two Colombian dogs with leishmaniasis and from an
Ethiopian rodent and sequenced. Chromosome-level
scaffolding and annotation was achieved through denovo assembly of the genome from paired-end Illumina Hiseq libraries coupled with iterative optimisation and correction procedures. Phylogenetic markers were extracted from the genomes and compared
with markers from a panel of known Leishmania
species, identifying two of them as members of the L.
braziliensis complex: L. naiffi and L. guyanensis and
the other as L. adleri, a member of the Sauroleishmania subgenus. All steps were tested and augmented
using the positive control of another Leishmania reference sequence (L. braziliensis [1] ) and it’s short
read data. This ensured the final draft genomes had
contiguity comparable with other high-quality published genomes. Short read coverage and allelic diversity determined variation across four levels in the
high quality draft genomes: ploidy, whole chromosome copy number, structural changes and SNPs. L.
naiffi, L. guyanensis and L. adleri were diploid but
aneuploidy, a rudimentary stress response also seen in
samples from human hosts, was observed in all three
species, illustrating the lack of differentiation between
parasites infecting humans and other animals, which
is a crucial factor for disease eradication programmes.
1 Rogers, M. B., Hilley, J. D., Dickens, N. J.,
Wilkes, J., Bates, P. a, Depledge, D. P., â Í
Mottram, J. C. (2011). Chromosome and gene
copy number variation allow major structural
change between species and strains of Leishmania. Genome Research, 21(12), 2129â 42.
doi:10.1101/gr.122945.111
Supported by NUIG College of Science funding
Research Day 2016: Posters
4
W per unit area of a membrane, given by
Lida Fallah
Supervisors: Prof. John Hinde, Dr. Haixuan Yang
Time to event, or survival, data is common in the biological and medical sciences. Here, we consider the
analysis of time to event data from two populations
undergoing life-testing, mainly under a joint Type-II
censoring scheme for heterogeneous situations, containing susceptible and non-susceptible items to failure. We consider a mixture model formulation and
maximum likelihood estimation using the EM algorithm and conduct a simulation to study the effect of
the form of censoring scheme on parameter estimation and study duration.
[1] Kuo, L. and Peng, F. (2000). A mixture-model
approach to the analysis of survival data. Generalized Linear Models: A Bayesian Perspective, (Eds. D. K. Dey, S. K. Ghosh and B. K.
Mallick), 255 – 267. New York: Marcel Dekker.
[2] Rasouli, A. and Balakrishnan, N. (2010). Exact
likelihood inference for two exponential populations under joint progressive Type-II censoring. Communications in Statistics- Theory and
Methods, 39, pp. 2172 – 2191.
Supported by the Irish Research Council.
Mathematical Modelling of
Nanoparticle Endocytosis
W=
kc
(2H ≠ c0 )2 + k̄K,
2
where c0 is the spontaneous curvature, H and K are
the mean and Gaussian curvatures, respectively, and
k̄, kc are the bending rigidities. While there are many
forces involved in the endocytosis process, including electrostatic, van der Waals, hydrophobic forces,
and receptor-ligand binding, these may be approximated as a single adhesion force which drives endocytosis. Mathematical modelling provides a rational
framework for the optimisation of this process. We
model this situation by assuming negligible tension
and spontaneous curvature, and taking the total energy to be the sum of the bending energy Ebe of the
membrane plus the adhesion energy Ead of the particles, where the bending energy is calculated as the
integral
⁄
Ebe = 2kc H 2 dA
over the area A of the membrane. For a particle
lengthscale of tens of nanometers, the adhesion potential is significant in the uptake process, and is taken
to be a Morse potential with characteristic potential
depth U , given by
V (d) = U (e≠2d/fl ≠ 2e≠d/fl ),
where d is the distance of the particle from the membrane and fl is the range of the adhesion potential. The adhesion energy is then given by Ead =
s
V (d) dA, which can easily be extended for a system of multiple particles.
Paul Greaney
Supervisors: Martin Meere, Giuseppe Zurlo, Yury
Rochev
[1] W. Helfrich. Elastic Properties of Lipid Bilayers: Theory and Possible Experiments, Z.
Naturforsch. C, 1973, 28 (11-12), 693-703.
Nanoparticles have been the subject of much recent
research due to their wide-ranging potential applications in areas such as high-resolution cellular imaging,
drug delivery, and tumour targeting. In general, the
uptake of such particles by cells occurs via endocytosis. The material to be taken up is surrounded by
a portion of the cell membrane, forming an invagination and eventually pinching off to form an endocytic
vesicle. In animal cells, receptor-mediated endocytosis is the mechanism which facilitates the uptake of
macromolecules via clathrin-coated pits and vesicles.
Macromolecules bind to transmembrane receptor proteins, which span from the exterior to the interior of
the cell membrane.
[2] S. Zhang, H. Gao, and G. Bao, Physical Principles of Nanoparticle Endocytosis, ACS Nano,
2015, 9 (9), 8655-8671.
The vast majority of biomembrane modelling is based
on the model proposed by Helfrich for the free energy
[3] M. Raatz, R. Lipowsky, and T. R. Weikl, Cooperative wrapping of nanoparticles by membrane
tubes, Soft Matter, 2014, 10, 3570-3577.
Supported by the College of Science, NUI Galway
Maximum rank of completions of
entry pattern matrices
Ha Van Hieu
Supervisors: Dr. Rachel Quinlan
Research Day 2016: Posters
Given a set S = {x1 , x2 , · · · , xk }, we denote by Mn (S),
or Mn (x1 , x2 , · · · , xk ) the set of n ◊ n matrices whose
entries are from S. The following definition appears
in [?].
Definition 1. Let x1 , x2 , · · · , xk be distinct indeterminates. We call a matrix in Mn (x1 , x2 , · · · , xk ) an
entry pattern matrix.
Thus an entry pattern is a matrix whose entries are
indeterminates some of which may be equal. The pattern class of an entry pattern matrix A, denoted by
CF (A), is the set of the matrices obtained by specifying the values of the indeterminates of A by elements
in some field F. Each element in CF (A) is called a
F-completion of A.
Definition 2. The maximum F-rank of A is the maximum rank of F-completions of A. The generic rank
of A is the rank of A when considered as a matrix in
Mn (F), where F is the field of rational functions in
the indeterminates that appear in A over F.
The maximum F-rank cannot exceed the generic rank
, and these are equal if the field F is big enough
or the number of indeterminates is smaller than 3.
This poster will present some precise conditions under which the maximum F-rank and the generic rank
coincide, and some constructions of examples over finite fields in which they differ.
[1] Z. Huang and X.Zhan, Nonsymmetric normal
entry patterns with the maximum number of
distinct indeterminates, Linear Algebra and its
Applications 485 (2015), 359-371.
Dynamic Nomograms
Amirhossein Jalali
Supervisors: Alberto Alvarez-Iglesias, John Hinde
and John Newell
In this poster I will introduce my ’DynNom’ package
in R which makes it possible to present the results of
statistical models as a dynamic nomogram that can
be interacted with in a web browser. Dynamic nomogram is a translational tool for the interpretability
it adds to a statistical model. It aims to facilitates
the integration of Biostatistics within clinical research
and enhance communication of research findings in an
accurate and accessible manner to diverse audiences
(e.g. policy makers, patients and the media). The
package allows an investigation into the results of the
proposed model, the relative importance of each explanatory variable (e.g. modifiable risk factors) and
an assessment of model assumptions through accompanying model diagnostics.
5
[1] Banks, J. (2006) Nomograms. Encyclopedia of
Statistical Sciences. 8.
[2] Jalali, A. et al. (2015) DynNom: Dynamic
Nomograms for Linear, Generalized Linear and
Proportional Hazard Models. R package version 2.0.
[3] Newell, J. Hinde, J. (2014) Translational Statistics and Dynamic Nomograms. Proceedings of
the Conference on Applied Statistics in Ireland
(CASI).
Penalized regression procedures with
multiply imputed data
Olga Kalinina
Supervisors: Dr. Emma Holia and Dr. John
Newell
Prognostic models play an important role in medical
decision making process. Missing predictors and censored responses are common problems within prognostic modelling studies. Simple methods, such as
complete cases analysis, are commonly used as the
default procedure in many statistical software packages. Several studies have shown that such approach
loses efficiency, and may lead to biased estimates if
there is a relationship between missing values and the
response. Multiple imputation is an attractive approach, which replaces each missing value in predictor by M credible values estimated from the observed
data. Then M imputed data sets are analysed separately and the parameters estimates and their standard errors combined using ’Rubin’s Rule’. However,
it is still unclear how to conduct variable selection
over multiply imputed data sets under the framework
of penalized regressions. Several methods have been
proposed and used in the literature. Wood(2008) performed classical backward stepwise selection method
where i) at each step, the inclusion and exclusion of
the variable is based on combined overall estimates
with standard errors using Rubin’s Rule, and ii) a
stacking method is used where the multiply imputed
data sets into one using a weighting scheme to account for the fraction of missing data in each explanatory variable. Chen(2013) and Wan(2015) proposed
methods combining multiple imputation and penalized regressions. Chen(2013) treated estimates from
the same variable across all imputed data sets as a
group, and applied the group lasso penalty to yield
a consistent variable selection, while Wan(2015) proposed weighted elastic net method to the stacking
Research Day 2016: Posters
method after multiple imputation with a weight accounting for the proportion of the observed information for each subject. Penalized regression techniques
like lasso, elastic net and group lasso achieve parsimony as they shrink some regression coefficients to
zero. However, it may lead to inconsistent variable
selection if they are applied directly to the multiply
imputed data sets.
[1] Chen Q, Wang S (2013). Variable selection
for multiply-imputed data with application to
dioxin exposure study. J Stat Comput Simulat
2015, 85(9), pp. 1902 – 1916.
[2] Wan Y, Datta S, Conklin DJ, Kong M (2015).
Variable selection models based on multiple imputation with an application for predicting median effective dose and maximum effect. Stat
Med 2008, 27, pp. 3227 – 3246.
[3] Wood AM, White IR, Royston (2008). How
should variable selection be performed with
multiply imputed data? Stat Med 2008, 27, pp.
3227 – 3246.
Gent models for the inflation of
spherical balloons
Robert Mangan
Supervisor: Michel Destrade
We revisit an iconic deformation of nonlinear elasticity: the inflation of a rubber spherical thin shell. We
find the link between the exact solution of nonlinear elasticity and the membrane and Young-Laplace
theories often used a priori in the literature. In particular, by expanding to first order in the thickness
parameter, we recover the classical relation T = P r/2,
where T is the wall tension, P is the internal pressure
and r is the radius of the sphere.
We use the 3-parameter Mooney and Gent-Gent phenomenological models to explain the stretch-strain
curve of a typical inflation, as these two models cover
a wide spectrum of known models for rubber, including the Varga, Mooney-Rivlin, one-term Ogden,
Gent-Thomas and Gent models. We find that the
basic physics of inflation exclude the Varga, one-term
Ogden and Gent-Thomas models. We compare the
performance of both models on fitting the data for
experiments on rubber balloons and animal bladder.
We conclude that the Gent-Gent model is the most
accurate and versatile model on offer for the modelling of rubber.
6
[1] R. Mangan, M. Destrade, Gent models for the
inflation of spherical balloons, International
Journal of Non-Linear Mechanics, 68 (2015),
52–58.
[2] W.A. Osborne, The elasticity of rubber balloons and hollow viscera, Proceedings of the
Royal Society of London, Series B, 81 (1909)
485–499.
Compact Homogeneous Spaces with
Positive Euler Characteristic and their
‘Strange Formulae’
Mohammad Adib Makrooni
Supervisor: John Burns
This poster presents my collaborative publication
with Dr. J. Burns [1]. In this research work, we prove
a generalisation of the ”Strange formula” of Freudenthal and de-Vries for compact homogeneous spaces
with positive Euler characteristic. We also apply the
results to computing a topological invariant used to
study hyper-Kähler structures. We also make use of
a sharpened version of Borel and de Siebenthal Theorem in [2], where the the isotropy representation of K
on the tangent space to G/K is described, in which
K denotes a maximal connected subgroup of maximal
rank in a compact simple Lie group G.
[1] J. M. Burns and M. A. Makrooni, Compact Homogeneous Spaces with Positive Euler Characteristic and their ‘Strange Formulae’, Quart. J.
Math. 66 (2015), 507-516.
[2] J.A. Wolf. Spaces of Constant Curvature,
McGraw-Hill. New York, 1967.
Deconvolution of genome-wide
epigenetic data from simulated
heterogeneous samples
Barbara Zambiasi Martinelli
Supervisors: Cathal Seoighe and Pilib à Broin
Biological samples are typically heterogeneous and in
many cases it is informative to determine differences
in the relative abundances of distinct cell types between groups of biological samples that display features of biological or biomedical interest. The state of
methylation in genomic sites characteristic of a specific cell type could be exploited to obtain highly accurate estimates of cell type proportions across samples by using statistical or mathematical methods.
Research Day 2016: Posters
7
Making use of the Expectation-Maximization (EM)
algorithm, and following the hypothesis that intermediate methylation/low entropy (IM/LE) loci are likely
to be highly informative for identifying and quantifying cell subtypes present in a meta-epigenome,
deconvolution of genome-wide epigenetic data can
be performed. In this work, whole genome bisulphite sequencing (WGBS) of two cell lines, IMR90
and NA12878, was used in the mixture simulation.
Firstly, all the CpGs of chromosome 21, the sequence
reads and their respective methylation status were retrieved. Simulated heterogeneous samples were generated by computationally mixing the methylation
data from the two cell lines in varying proportions.
Percentage of methylation in each CpG of the mixture was calculated and, using a sliding window approach, genome regions with IM were identified. For
this step, the parameters were settled as: a) window
size of 10 CpG sites, b) window shift of 1 site, c)
methylation values between 30
Propensity Score Matching Methods
for Observational Studies
Michael Mc Cague
Supervisors: Dr. John Newell
Propensity Score Matching is an increasingly popular
statistical concept used as a pre-processing step for
causal inference in observational studies. The goal is
to match subjects in the case and control groups as
closely as possible on their given observed characteristics so as to approximate the conditions of a randomised controlled trial to better estimate the true
’treatment’ effect of being in the case group. There
are many different matching algorithms and settings
advocated in current literature and in this poster, using a sample of data arising from an observational
study, I will present a comparative study of some of
these methods and their merits relative to when no
matching is performed, aided by graphical summaries
using R and Tableau software.
[1] Rosenbaum, P. R. and Rubin, D. B. (1983b).
The central role of the propensity score in observational studies for causal effects. Biometrika
70, 41â 55.
[2] Ho DE, Imai K, King G, Stuart EA.
MatchIt:
nonparametric preprocessing for
parametric causal inference. J Stat Software
2011;42:1â 28.
[3] Stuart, Elizabeth A. 2010.
â
Methods for Causal Inference:
Matching
A Review
and a Look Forward.â
25(1):1â 21. (CASI).
Statistical Science
A Bayesian approach to imputation of
survival data
Shirin Moghaddam
Supervisors: Prof. John Hinde, Dr. Milovan
Krnjajić and Dr. John Newell
In survival analysis, due to censoring, standard methods of plotting individual survival times are invalid.
Therefore, graphical display of time-to-event data
usually takes the form of a Kaplan-Meier survival
plot. By treating the censored observations as missing
and using imputation methods, a complete dataset
can be formed. Then standard graphics may usefully
complement Kaplan-Meier plots. Here, we consider
using a Bayesian framework to present a flexible approach to impute the censored observations using predictive distributions.
[1] Christensen, R. et al. (2010).Bayesian Ideas
and Data Analysis: an introduction for scientists and statisticians. CRC Press.
[2] Lunn, D. et al. (2012). The BUGS Book:
A Practical Introduction to Bayesian Analysis.
CRC Press.
[3] Royston, P. et al. (2008). Visualizing length
of survival in time-to-event studies: a complement to Kaplanâ Meier plots. Journal of the
National Cancer Institute, 100, pp. 92 – 97.
Analysis of Allele Specific Translation
across Human Individuals
Ngoc Nguyen
Supervisors: Cathal Seoighe
Genetic variants are considered as an important
source of phenotypic variations and may give rise
to human genetic diseases and complex phenotypes.
Allele specific translation (AST) analysis, a method
integrating genome and transcriptome data has become an important tool for studying genome function, because it quantifies the differences in protein
production efficiency between alternative alleles of
a gene distinguished by heterozygous sites. Several
studies presented integrative analysis of RNA-seq and
ribosome profiling data to reveal distinct regulatory
genetic variants that can impact protein abundance
Research Day 2016: Posters
through their effect on translation (Battle et al. 2015;
Albert et al. 2014; Cenik et al. 2015). However, unavoidable presence of PCR artifacts (introduced in
library amplification process) is the most common issue in ribosome profiling data, which can confound
downstream AST analysis and up-to-date, there is
still no correction method suggested for it. Here we
presented the initial analysis of transcriptomic and
ribosome profiling datasets from lymphoblastoid cell
lines (LCLs) samples of 60 individuals to reveal a list
of SNPs that potentially causing and/or associated
with human diseases and complex phenotypic traits.
Moreover, we also demonstrated the inspection of systematic bias introduced by PCR artifacts across samples.
[1] Albert FW, Muzzey D, Weissman JS, Kruglyak
L. 2014. Genetic Influences on Translation in
Yeast. PLoS Genet 10: e1004692.
[2] Battle A, Khan Z, Wang SH, Mitrano A, Ford
MJ, Pritchard JK, Gilad Y. 2015. Impact of
regulatory variation from RNA to protein. Science 347: 664?667.
[3] Cenik C, Cenik ES, Byeon GW, Grubert F,
Candille SI, Spacek D, Alsallakh B, Tilgner H,
Araya CL, Tang H, et al. 2015. Integrative
analysis of RNA, translation, and protein levels reveals distinct regulatory variation across
humans. Genome Res.
8
Rigidity of Surface Graphs
Qays Shakir
Supervisor: James Cruickshank
This poster presents a survey of some of the key concepts of geometric rigidity theory. In the case of bar
and joint frameworks, the three dimensional rigidity
problem remains one of the major open problems in
the area. We propose to investigate this problem in
the special case of graphs that are derived from triangulations of surfaces.
[1] A. Nixon,E. Ross, One brick at a time: a survey of inductive constructions in rigidity theory,
Rigidity and symmetry, 22 (2014) , 303-324.
[2] H, Gluck. Almost All Simply Connected Closed
Surfaces are Rigid.
Heidelberg, Germany:
Springer-Verlag, (1975) 225-239.
[3] W. Whiteley, Vertex splitting in isostatic frameworks, Structural Topology,16 (1991), 23-30.
[4] J. Cruickshank D. Kitson, S. Power, The
Generic Minimal Rigidity of a Partially Triangulated Torus, to be appear.
This project is supported by Irish Research Council
Adaptive Ranges for Clinical
Biomarkers using Bayesian Approaches
Minimal Graphs of Exponent 2
Davood Roshan Sangachin
Supervisors: Dr. John Newell, Prof. Fracis J.
Sullivan
Olga O’Mahony
Supervisor: Dr Rachel Quinlan
A non-negative matrix A is called primitive if Ak is
positive for some positive integer k; the least such k is
called the exponent of A. A graph is said to be primitive of exponent k if its adjacency matrix is primitive
of exponent k. If u and v are vertices of such a graph
G, then there exists a path of length k from u to v in
G.
We say a graph G is minimal of exponent 2, or is an
me2 graph, if G has exponent 2, and if you delete any
edge, then G no longer has exponent 2.
This poster deals with the problem of efficiently embedding a tree as an induced subgraph of an me2
graph. We present a theorem, and give an example
to show how to construct an efficient embedding.
Supported by The College of Science NUIG
Biomarkers are measurements reflecting an interaction between a biological system and a potential hazard. They are typically measured and evaluated as
indicators of normal/abnormal biological processes.
Biomarkers may be measured on a bio-sample (e.g.
blood), may be a recording (e.g. blood pressure),
or an imaging test (e.g. echocardiogram). Ascertainment of the pattern and temporal changes of biomarkers play a vital role as indicators of risk markers, disease state or disease progression.
A reference range, generated from a cross-sectional
analysis of healthy individuals free of the disease of
interest, is typically used as a basis for comparison to
interpret a set of test results for a particular patient.
An arbitrary percentile cut-point (typically the 95th
or 97.5th percentile) is chosen to define abnormality. When biomarkers are collected longitudinally for
Research Day 2016: Posters
patients, dynamic reference ranges are needed for effective diagnosis which adapt to account for between
and within subject variability.
In this poster, methods for generating adaptive
ranges using tolerance intervals and Bayesian approaches are discussed. Initially the patient specific
reference range is based on the tolerance interval generated for the population in question which adapts
over time as more data are collected for that individual. These adaptive ranges have the potential to
detect a meaningful change earlier.
This methodology will be applied to the construction of adaptive range for Prostate Specific Antigen
(PSA) biomarker in patient with prostate cancer and
in blood testing in elite athletes.
[1] Sottas P, Baume N, Saudan C, Schweizer
C, Kamber M, Saugy M. (2007). Bayesian
detection of abnormal values in longitudinal
biomarkers with an application to T/E ratio.
Biostatistics, Volume 8, pp. 285 - 296
[2] Zorzoli M. (2011). Biological passport parameters. Journal of Human Sport and Exercise,
Volume 6, pp. 205-217.
Hochschild cohomology rings of
algebras k[x1 , . . . , xn ]/(x1 . . . xn )
Tran Thi Hieu Nghia
Supervisors: Dr. Emil Sköldberg, Dr. Alexander
D. Rahm
Let k be a commutative ring with unity and f in
k[x] a monic polynomial. The ring structure of the
Hochschild cohomology for the k-algebra k[x]/(f )
was determined (in [1]). We want to consider this
problem in a more general case, for the algebra
k[x1 , . . . , xn ]/(x1 . . . xn ). In this poster, we review the
basic definitions of Hochschild cohomology for algebras and describe some early results on this research
problem. The results are in a joint work with Emil
Sköldberg and Isaac Burke.
[1] Th. Holm, Hochschild cohomology rings of algebras k[X]/(f ), Contributions to Algebra and
Geometry, Vol. 41, No. 1, pp. 291 - 301 (2000).
[2] J. A. Guccione, J. J. Guccione, M. J. Redondo,
O. E. Villamayor, Hochschild and Cyclic Homology of Hypersurfaces, Advances in Mathematics 95, pp. 18 - 60 (1992).
Supported by The College of Science, National University of
Ireland, Galway.
9
Genus Two Zhu Theory for Fermionic
Vertex Operator Superalgebras
Michael Welby
Supervisors: Prof. Michael Tuite
The theory of n-point functions for a Vertex Operator (Super-)Algebra (VO(S)A) has been welldocumented at genus zero and one. These functions
have a natural description in terms of functions from
classical number theory. The theory is that there is a
higher genus analogue of these objects, following the
results of Zhu [3], who developed a recursion formula
relating n-point functions to (n ≠ 1)-point functions
at genus one.The aim of the project is essentially to
generalise the results of [2] to a genus two environment, that is: Zhu recursion on a genus two VOSA.
Higher genus versions of the objects such as “twisted
Weierstrass functions” are expected be found, which
will have some relation to forms on the genus two surface. These functions should play a role in the Zhu
reduction of genus two VOSA n-point functions.
1 T. Gilroy, M.P. Tuite: Genus Two Zhu Theory
for Vertex Operator Algebras, arXiv 1511.07664
.
2 G. Mason, M.P. Tuite and A. Zuevsky: Torus
n-point functions for R-graded vertex operator
superalgebras and continuous fermion orbifolds,
Commun.Math.Phys. 283 (2008) 305-342.
3 Y. Zhu.: Modular invariance of characters of
vertex operator algebras, J. Amer.Math.Soc. 9
(1996) 237-302.
LymAnalyzer: a tool for
comprehensive analysis of next
generation sequencing data of T cell
receptors and immunoglobulins.
Yaxuan Yu
Supervisors: Rhodri Ceredig, Cathal Seoighe
The adaptive immune system includes populations
of B and T cells capable of binding foreign epitopes
via antigen specific receptors, called immunoglobulin
(IG) for B cells and the T cell receptor (TCR) for T
cells. In order to provide protection from a wide range
of pathogens, these cells display highly diverse repertoires of IGs and TCRs. This is achieved through
Research Day 2016: Abstracts of PhD and MSc Theses
combinatorial rearrangement of multiple gene segments in addition, for B cells, to somatic hypermutation. Deep sequencing technologies have revolutionized analysis of the diversity of these repertoires; however, accurate TCR/IG diversity profiling requires specialist bioinformatics tools. Here we
present LymAnalzyer, a software package that significantly improves the completeness and accuracy
of TCR/IG profiling from deep sequence data and
includes procedures to identify novel alleles of gene
segments. On real and simulated data sets LymAnalyzer produces highly accurate and complete results.
Although, to date we have applied it to TCR/IG
data from human and mouse, it can be applied
to data from any species for which an appropriate
database of reference genes is available. Implemented
in Java, it includes both a command line version and
a graphical user interface and is freely available at
https://sourceforge.net/projects/lymanalyzer/.
[1] Yu, Yaxuan, Rhodri Ceredig, and Cathal
Seoighe. ”LymAnalyzer: a tool for comprehensive analysis of next generation sequencing data
of T cell receptors and immunoglobulins.” Nucleic acids research (2015): gkv1016.
10
3
Abstracts of PhD Theses
Analysis and Interpretation of Epigenomic Patterns
in Colonic Epithelia
Alan Barnicle
Supervisor: Laurence Egan and Cathal Seoighe
The methylation of cytosine nucleotides at the 5’ position of DNA is a crucial epigenetic mechanism for
the control of gene expression. Epigenome-wide associated studies have demonstrated that specific methylome patterns exist in certain disease states, that
methylome signatures can predict cancer susceptibility and that methylation patterns are capable of characterizing epigenomic events that stimulate the survival of cancer cells. Little is known about the effect
of chronic inflammation on DNA methylation.
In this work, we analysed the effect of chronic inflammation on DNA methylation patterns in ulcerative
colitis (UC), a condition that predisposes to colon
cancer. Due to the cell type specific nature of DNA
methylation patterns, this PhD initially focussed on
designing an epithelial cell isolation method that was
capable of enriching a purified epithelial population
both in diseased and non-diseased states. Secondly,
we wished to test the hypothesis that distinct colonic
regions have specific methylation signatures, while
also comparing DNA methylation patterns in isolated
epithelial cells and in whole colonic mucosal biopsies.
Finally, using the chronic inflammatory condition of
ulcerative colitis (UC) as a pathogenic phenotype,
this PhD aimed to identify potential epigenomic and
genomic dysregulation that occurs in intestinal epithelial cells in inflamed areas of the colon.
Isolation of epithelial cells from mucosal biopsies resulted in purified populations of crypts consisting of
90% pure epithelium. Using these fractions isolated
at 4Â C to minimize degradation of nucleic acids, it
was demonstrated that stable and integral mRNA
and gDNA could successfully be extracted in both
diseased and non-diseased states. Using genome-wide
technology, specific DNA methylation signatures in
the proximal and distal colon in samples from healthy
colon were identified. Computational deconvolution
was also used to characterize accurate epithelial cell
estimates from whole colonic biopsies, while also highlighting the increased DNA methylation variability
caused by samples comprised of a mixture of cell
lineages. Results from this study identified regionspecific epigenomic patterns of HOX genes (specifically HOXB and HOXC families). These patterns
represent a valuable tool for interpreting experimental data on diseases that exhibit region-specific expression in the colon such as inflammatory bowel disease and colorectal cancer. By performing genome-
Research Day 2016: Abstracts of PhD and MSc Theses
wide DNA methylation and transcriptome profiling
of purified intestinal epithelial cells, it was demonstrated that significant DNA methylation and gene
expression variation occurs in UC. Genes showing inverse correlation between DNA methylation and gene
expression levels were also identified, most notably
promoter hypermethylation and down regulation of
RARB. This gene was previously identified as a tumour suppressor in colorectal adenocarcinoma as well
as in breast, lung and prostate cancer. However this is
the first finding of RARB potentially playing a functional role in UC. This integrative epigenomic dataset
will enhance our understanding of UC pathophysiology, potentially adding to our knowledge of the links
between chronic inflammation and carcinogenesis.
The Genomic Architecture of Nucleolar Organiser
Regions on the Short Arms of Human Acrocentric
Chromosomes
Sofia Nazarà de Pereira Barreira
Supervisor: Brian McStay and Cathal Seoighe
Nucleolar Organiser Regions (NORs) are comprised
of ribosomal gene (rDNA) arrays and adjacent sequences. Nucleoli, the sites of ribosome biogenesis
and key regulators of cellular growth and proliferation, form around NORs. In humans, NORs are
positioned on the short arms of the five acrocentric
chromosomes (13, 14, 15, 21 and 22). These chromosome arms are not included in the human reference
genome and have only recently started to be mapped
and characterised.
This thesis has focussed on contributing to the characterisation and extension of these underexplored genomic regions. Previous work had suggested that as
many as one third of rDNA repeats are rearranged.
These could impact on nucleolar and ribosomal formation and protein synthesis. By performing next
generation sequencing on DNA extracted from purified nucleoli, I demonstrated that there is no evidence for rearranged rDNA repeats in human cell
lines. This conclusion was emphasised by a detailed
analysis of more recent long read DNA sequence data
sets. The second objective of this thesis was to describe the spatial organisation of sequences distal to
the clusters of rDNA repeats. These sequences exhibit a euchromatic-like chromatin organisation, are
transcriptionally active and appear to function as an
anchor for the linked rDNA array during interphase.
In the post genomic age, much effort now focuses on
describing the chromatin status and 3D organization
of the genome in a variety of human cell types and
it is common practice to make the raw sequencing
11
data from these genome-wide studies publicly available. Exploiting Hi-C data sets designed to capture
genome organisation revealed the existence of a transcription dependent stem-loop structure encompassing over 200 kb of NOR distal sequence that may play
a role in NOR regulation. The third objective was to
extend the sequences distal to NORs and characterise
them. Using a combination of nucleolar sequencing
reads and Hi-C data, this region was extended by 180
Kb. Analysis of data from the ENCODE project suggests that this region is transcriptionally active and
marks the beginning of interchromosomal variability
on the short arms of acrocentric chromosomes.
These results provide a platform for investigating the
role of NORs in nucleolar formation and maintenance
and serve as a starting point for the identification and
characterisation of the unknown regions of the p-arms
of acrocentric chromosomes.
Theoretical and numerical analysis of rigid-body
impacts with friction
Shane Burns
Supervisor: Dr Petri Piiroinen
This thesis gives a flavour of the area of rigid body impacts with friction, an area which has far reaching applications in engineering, sports science and every day
life. The focus of this work will be on the two main
streams of this field, theoretical and numerical. This
thesis will present an overview of the general subject
of rigid-body impact, including discussion and analysis of the validity of ones choice of impact law and
the numerical techniques required for the simulation
of rigid-body impacting systems.
Two impact laws will be introduced in Chapter 3 and
a direct comparison will be made in order to examine
the varying dynamics that can be achieved using both
a basic and a complex impact law and to explore some
of the problems that can occur with a more basic
formulation. It will be demonstrated that for certain
regions in parameter space the two formulations are
equivalent, however, for many other regions the two
formulations can vary greatly.
A hybrid event-driven numerical scheme is one in
which smooth dynamics are described by differential equations, which can be solved numerically using
standard techniques, and non smooth events which
are described my maps. In Chapter 5, a hybrid eventdriven numerical scheme for the implementation of
the Energetic impact law described in Chapter 3 is
presented. Moreover, the framework necessary for the
long term simulation of mechanical systems with impacts and chatter is derived.
Research Day 2016: Abstracts of PhD and MSc Theses
This thesis also gives an overview of the phenomena known as the Painlevé Paradox in Chapter 6 and
presents a numerical experiment to show the occurrence of the paradox for a mechanical system.
Mathematical models of seasonal migration
John Donohue
Supervisor: Dr Petri Piiroinen
The phenomenon of seasonal migration has attracted
a wealth of attention from biologists. However, the
dynamics of migratory populations have been little
considered. In this thesis, we use differential equations to model the variation in abundance of seasonally migrating populations.
Our contribution to the field begins with a representation of seasonal breeding. We use piecewise-smooth
differential equations to model the variation in the
size of a population that has a short interval each
year during which successful reproduction is possible.
We first consider a one-species model which illustrates
the dynamics of a population of specialist feeders over
the course of a single breeding season and use it to examine how reproductive success depends on the population’s distribution of breeding dates. We then introduce time-dependent switches to extend the model
to a broader class of species. This allows us to consider the effect of climate change on populations that
annually travel long distances.
We then shift focus to consider interactions between
migrants and species at higher levels in the food web.
Predatory pressure influences almost all populations
to some extent. Here, however, interactions may occur for just a brief period each year before the populations involved become spatially separated. The range
of a migrating population may overlap with that of
a population of predators for a single season. We
outline a framework for examining how this kind of
“transient” predation influences the dynamics of the
prey population. We are then able to examine how
a migratory population may be overwhelmed by the
fleeting influence of members of other species.
Finally, as an alternative to the aforementioned models, we outline a different approach to modelling migration, namely using partial differential equations
instead of ordinary differential equations. In this way,
we provide two distinct templates for the future exploration of the dynamical features of such populations.
Incremental elastic surface waves and static wrinkles
12
Artur L. Gower
Supervisor: Professor Michel Destrade
This article-based thesis comprises a collection of four
articles, each of which constitutes a chapter written
and formatted in manuscript form. The general aim
underlying these articles is to understand and predict
how incremental elastic surface waves propagate or
static wrinkles form on a deformed elastic substrate.
The formation of these small-amplitude disturbances
can be the end goal, such as in sending signals or
creating functional coatings, or they can be used to
measure and characterise the underlying elastic substrate. This thesis focuses on using surface waves or
static wrinkles to characterise soft solids, such as biological tissues.
Chapter 1 predicts a new phenomenon: oblique wrinkles, which should appear in a large range of materials. Yet oblique wrinkles have not been seen experimentally so far on soft solids. Another issue raised
was why are the predicted critical strains greater
than the experimentally observed critical strains? We
showed that this is likely due to a skin effect caused
by dehydration.
In Chapter 2 the effects of a stiffer skin on an elastic
substrate on surface wrinkles was initially studied,
and therein we also studied the possibility of using
surface wrinkles to characterise fibre reinforced materials.
The results from Chapter 3 show that measuring
the propagation speed of surface waves only along
the principal directions of deformation leads to many
challenges in non-destructive evaluation of strain and
stress, because these directions are not necessarily
aligned with the directions of fastest and slowest
propagation. However, the methods for calculating
surface waves along any direction presented in that
chapter are now sufficiently mature and robust to be
able to use the full Rayleigh wave-field in order to
characterise solids. There are now experiments in
place that measure surface waves on tissue, and a
wide range of techniques to infer the surface elastic
properties from these measurements for a range of
materials. Yet, to date, surface wave measurements
have not been adequately linked to the elastic properties of soft tissue, such as the residual stress or the
reinforcing fibre properties.
Chapter 4 shows a surprisingly simple relationship between the angle of the surface wrinkle wave-front and
the fibre orientation, a trend which becomes stronger
the stiffer the fibres. Yet predicting how these wrinkles appear on soft fibre reinforced solids required a
highly technical and involved numerical method. A
promising alternative model is that of a soft tissue
Research Day 2016: Abstracts of PhD and MSc Theses
13
reinforced by fibres idealized to be infinitely stronger
than the surrounding soft matrix.
[2] We devise and implement an algorithm for computing a finite ZG-equivariant CW-space with
nice cell stabilizer groups and a contracting discrete vector field, where G = SL2 (Z[1/m]) for
any positive integer m. (See Algorithm 3.2.1.)
Completions of Partial Matrices
[3] We implement a function which inputs a nonfree ZG-resolution and outputs finitely many
terms of a free ZG-resolution Rú of Z, where
G = SL2 (Z[1/m]) for any positive integer m.
(See Algorithm 2.1.1.)
James McTigue
Supervisor: Rachel Quinlan
A partial matrix over a field F is a matrix whose entries are either elements of the field or independent
indeterminates. A completion of a partial matrix is
any matrix that results from assigning a field element to each indeterminate. The set of completions
of an m ◊ n partial matrix forms an affine subspace
of Mm◊n (F).
[4] We devise and implement an algorithm for
computing finitely many terms of a free ZHresolution Rú of Z for H a finite index subgroup
of G = SL2 (Z[1/m]). (See Algorithm 3.2.2.)
[5] We devise and implement an algorithm that attempts to find a cubical fundamental cell for
a cubical crystallographic group G. (See Algorithm 4.3.1).
This thesis investigates partial matrices whose sets of
completions satisfy particular rank properties - specifically partial matrices whose completions all have
ranks that are bounded below and partial matrices
whose completions all have the same rank. The maximum possible number of indeterminates in such partial matrices is determined, and the partial matrices
that attain these bounds are fully characterized for
all fields. These characterizations utilize a duality
between properties of affine spaces of matrices that
are related by the trace bilinear form.
[6] We devise and implement an algorithm that inputs a crystallographic group G together with
a cubical fundamental cell and outputs a finite
ZG-equivariant CW-space with nice cell stabilizer groups and a contracting discrete vector
field. (See Algorithm 4.4.1).
[7] We implement a function for calculating finitely
many terms of a free ZG- resolution Rú of
Z with contracting homotopy, where G is an
n-dimensional cubical crystallographic group.
This resolution can be used to compute the cohomology ring structure of G. (See Algorithm
4.5.1.)
Precise conditions (based on field order, rank and
size) are provided to determine if a partial matrix
whose completions all have rank r must possess an
r ◊r partial submatrix whose completions are all nonsingular.
Finally a characterization of maximal nonsingular
partial matrices is provided - a maximal nonsingular partial matrix is a square partial matrix each of
whose completions has full rank, with the property
that replacement of any constant entry with an indeterminate results in a partial matrix having a singular
completion.
[8] We give the complete list of 3-dimensional cubical Bieberbach groups with their cohomology
ring structures.(See Section 4.7.)
4
Discrete vector fields and cohomology of certain
arithmetic and crystallographic groups
Bui Anh Tuan
Supervisor: Graham Ellis
This thesis makes the following contributions to the
area of Computational Algebraic Topology:
[1] All algorithms written in this thesis are implemented and are publicly available as documented functions for the GAP computer algebra system, and are distributed with the system
as part of its HAP package.
Abstracts of Masters Theses
Ability to construct mathematical proof at senior
Irish undergraduate level: a qualitative study
Michelle Duane
Supervisor: Dr Aisling McCluskey
This research uses a qualitative approach to investigate senior Irish undergraduate mathematics studentsÂü approaches to proof construction in the analytical subject metric spaces. In particular, the study
is concerned with the impact that logical statements
have on a studentÂüs ability to succeed in proofmaking.
Research Day 2016: Research Activity
First, a review of the literature looks at the relevant
areas of research: approaches to proof construction,
the role of intuition and informal representations in
the proving process, and undergraduate studentsÂü
difficulties in constructing proofs.
The qualitative research was carried out by means
of audio-recorded task-based inter- views with six
participants from the mathematics module Metric
Spaces, at National University of Ireland, Galway
during 2013. The students were in the penultimate
or final year of their chosen degree programme. Participants were asked to write down and discuss their
ideas for proofs relating to a number of different tasks
provided. The tasks were designed with particular
focus on the logical form of mathematical statements
and to be accessible without reliance on memory. All
relevant mathematical definitions were provided to
the students at the interviews. The interviews were
transcribed and coded inductively from the  bottom
upÂö, using a grounded-theoretic approach.
The analysis of interview data provides some evidence
to suggest that students possess a number of difficulties in working with implications and notably with
those that include universally quantified statements.
In particular, students in general placed disproportionate emphasis on the hypotheses of implications,
while simultaneously ignoring the chosen goals. Students also showed difficulty in working with particular mathemati- cal definitions, like continuity and
sequential convergence, when trying to create valid
proofs. The research also suggests that some students
have a concept image of proof by contradiction that is
linked to the notions of converse or counterexample,
and that this indirect proof method is not properly
understood, in general.
Superconformal Symmetry in Vertex Operator
Super Algebras
Philip Vernon
Supervisor: Prof Michael Tuite
This thesis gives a brief review of Vertex Algebras
and Vertex Operator Algebras and discusses their relationship with modular forms and elliptic functions.
We also investigate super-symmetric extensions of
the celebrated Virasoro algebra, namely the NeveuSchwarz N = 1, N = 2 and N = 4 super-conformal
algebra. We also construct fermionic models for each
of these super-conformal Vertex Operator Super Algebras.
14
5
Research Activity from 1 Jan
2015 to 31 Dec 2015
Permanent and Contract Staff
Burns, John
Current Research Interests
My current research interests are Algebra (Lie algebras, Lie groups, Weyl groups) and Differential Geometry (Homogeneous manifolds, Symmetric spaces).
Research in these areas is ongoing with various authors:
Adib Makrooni and I are studying relations between
root theoretic data, such as the Coxeter number and
the exponents, of parabolic sub-root systems and
those of the parent root systems. Applications include formulae for the defect of projective varieties.
Patrick Browne and I are working on graded Lie Algebras and their application to the geometry of homogeneous submanifolds of noncompact symmetric spaces.
These spaces are interesting as they contain a large
class of Einstein manifolds.
Publications
Most significant recent publications
[1] Burns, John M.; Makrooni, Mohammad A.
Compact homogeneous spaces with positive Euler characteristic and their ‘strange formulae’.
Q. J. Math. 66 (2015), no. 2, 507?516.
Research Activities
// Invited talks: Workshop on Geometry,
U.C.C. Boole celebrations Oct. 2015. //Refereeing: 1 paper. //Reviewing: 1 paper.
//Conferences and workshops: Irish Geometry
Conference (Limerick) 2015. Groups in Galway, May 2015. //Postgraduate supervision: 1
Ph.D. student.
1. Burns, John M.; Makrooni, Mohammad A. Compact homogeneous spaces with positive Euler characteristic and their ‘strange formulae’. Q. J. Math. 66
(2015), no. 2, 507?516.
2. Maximal Order Abelian Subgroups of Coxeter
Groups as Discrete Maximal Tori (with G. Pfeiffer).
Available at arXiv:1601.07812
3. Parabolic Sub-root Systems (with M. Makrooni)
Research Day 2016: Research Activity
Cruickshank, James
Current Research Interests
[1] Geometric graph theory - in particular rigidity
of bar-joint frameworks and other related structures.
[2] Random geometric graphs.
Publications
No publications appeared in 2015. Two papers accepted for publication during 2015:
• Cruickshank, James; Loane, John; Ryan, Ray.
Positive polynomials on Riesz spaces. Accepted
by Positivity subject to minor changes
• Cruickshank, James; Kitson, Derek; Power,
Stephen. The generic rigidity of triangulated
spheres with blocks and holes. Accepted by
Journal of Combinatorial Theory, Series B subject to minor changes.
Research Activities
Graduate Students: Qays Shakir, Christine Marshall
(cosupervised with Colm O Riordan, Discipline of Information Technology)
Conferences:
• Rigidity Workshop, Lancaster University, June
2015. (Invited speaker).
• Geometric Rigidity Workshop, Banff International Reseach Station, July 2015 (Invited
speaker).
• Global Rigidity Workshop, Banff International
Research Station, July 2015 (participant).
Editorships: Editorial board of the Bulletin of the
IMS
Journal Submissions: 1 paper to Discrete and Computational Geometry.
Destrade, Michel
Current Research Interests
I apply the principles of Continuum Mechanics to the
modelling of soft matter, including soft silicones, gels,
and biological tissues such as the human skin and
brain matter. I am mainly working in problems and
applications of elastic wave propagation, elastic stability, and proper computational solid mechanics.
15
Publications
Number of publications appearing in calendar year
2015: seven articles in international scientific journals.
Most significant recent publications
[1] A.L. Gower, P. Ciarletta, M. Destrade. Initial
stress symmetry and its applications in elasticity, Proceedings of the Royal Society A, 471
(2015) 20150448.
[2] Y. Jiang, G. Li, L.-X. Qian, S. Liang, M. Destrade, Y. Cao. Measuring the linear and nonlinear elastic properties of brain tissue with
shear waves and inverse analysis, Biomechanics and Modeling in Mechanobiology 14 (2015)
1119-1128.
[3] M. Destrade, M.D. Gilchrist, J.G. Murphy,
B. Rashid, G. Saccomandi. Extreme softness
of brain matter in simple shear, International
Journal of Non-Linear Mechanics, Special Issue
in Honour of Martine Ben Amar [invited contribution] 75 (2015) 54-58.
[4] R. Mangan, M. Destrade, Gent models for
the inflation of spherical balloons, International
Journal of Non-Linear Mechanics, Special Issue
in Honour of Alan Gent [invited contribution]
68 (2015) 52-58.
The three (or fewer) pieces of work published during
2013-2017 that I plan to submit to the internal review
of the school’s research next year.
[1] L. Vergori, M. Destrade, P. McGarry, R.W.
Ogden. On anisotropic elasticity and questions concerning its Finite Element implementation, Computational Mechanics, 52 (2013)
1185-1197.
[2] A.L. Gower, P. Ciarletta, M. Destrade. Initial
stress symmetry and its applications in elasticity, Proceedings of the Royal Society A, 471
(2015) 20150448.
[3] Y. Jiang, G. Li, L.-X. Qian, S. Liang, M. Destrade, Y. Cao. Measuring the linear and nonlinear elastic properties of brain tissue with
shear waves and inverse analysis, Biomechanics and Modeling in Mechanobiology 14 (2015)
1119-1128.
Research Activities
Research grants: COST Action/European Science
Foundation (Co-I, unsuccessful), Postgraduate
Research Day 2016: Research Activity
Hardiman Fellowship for Robert Mangan (unsuccessful), Postgraduate IRC Fellowship for Robert
Mangan (successful), NUI Galway start-up grant
(PI), NUI Galway College of Science Scholarship
for Robert Mangan (declined), NUI Travelling
Scholarship for Robert Mangan (shortlisted), Italian
Institute of Higher Mathematics INdAM Visiting
Professor Programme (PI).
Numbers of graduate students: 1 (Artur Gower and
then, Robert Mangan);
Research Fellow:
1 (Valentina Balbi) Conferences/Seminars: 18;
Outreach talks: 10;
Research Visits: 4 (Modena, Tianjin, Glasgow,
Manchester);
Research Visitors: 5 (Saccomandi/Perugia, Vergori/Glasgow,
Napoli/Lecce,
Carfagna/Turin,
Su/Hanzhou);
Papers refereed: 14;
International Grant referee: 2 (International Centre
for Mathematical Sciences, Tec 21 Laboratory of
Excellence);
PhD External Examiner: 1 (Paris 6);
Professorial Promotion External Examiner: 1 (Milan);
Editorial Board Member: 6 (Proceedings of the
Royal Society A, Quarterly Journal of Mechanics
and Applied Mathematics, International Journal of
Applied Mechanics, International Journal of NonLinear Mechanics, Journal of the Acoustical Society
of America, SIAM Journal of Applied Mathematics);
Memberships: Acoustical Society of America, Society
for Industrial and Applied Mathematics, International Society for the Interaction of Mechanics and
Mathematics;
External positions: Reviews Editor (Proceedings of
the Royal Society A); Contributing Editor (International Journal of Non-Linear Mechanics); Visiting
Professor of Mechanical Engineering (University
College Dublin); Directeur de Recherche, Institut
d’Alembert, CNRS, Paris, France (on leave); International Brain Mechanics and Trauma Lab (Oxford);
Biomechanics Research Centre (NUI Galway).
Dooley, Cara
Current Research Interests
My research interests include design and analysis
of observational studies and analysis of longitudinal
data, survey data and survival data.
16
Publications
4 publications were published in 2015 with a further
two in press. Most significant recent publications
[1] Donoghue OA, Jansen S, Dooley C, De Rooij S,
Van Der Velde N, Kenny RA. 2014. Atrial Fibrillation Is Associated With Impaired Mobility
in Community-Dwelling Older Adults. Journal
of the American Medical Directors Association.
15(12) (2015)929â 933.
[2] Akuffo, KO, Nolan, J, Stack, J, Moran, R,
Feeney, J, Kenny, RA, Peto, T, Dooley, C,
O’Halloran, AM, Cronin, H, Beatty, S. Prevalence of age-related macular degeneration in the
Republic of Ireland. British Journal of Ophthamology. 99(8) (2015) 1037-1044.
[3] McCrory, C., Dooley, C., Layte, R.& Kenny,
R.A. The Lasting Legacy of Childhood Adversity for Disease Risk in Later Life. Health Psychology 34(7) (2015) 687-696.
[4] O’Sullivan, V, Nolan, B, Barrett, A, Dooley, C.
2014. Income and Wealth in the Irish Longitudinal Study on Ageing. Economic and Social
Review 45(3) (2015) 329-348.
Ellis, Graham
Current Research Interests
I am interested in computational algebraic topology,
and particularly in: (i) calculations related to the cohomology of discrete groups and; (ii) calculations of
homotopy theoretic invariants of topological spaces
arising from scientific data sets.
Publications
Most significant recent publications
[1] Brendel, Piotr; Dlotko, Pawel; Ellis, Graham;
Juda, Mateusz; Mrozek, Marian. Computing
fundamental groups from point clouds. Appl.
Algebra Engrg. Comm. Comput. 26 (2015),
no. 1-2, 27-48.
[2] Ellis, Graham; Murillo, Aniceto; Real, Pedro;
Sáenz-de-Cabezón, Eduardo. Editorial [Computational algebraic topology and its applications]. Appl. Algebra Engrg. Comm. Comput.
26 (2015), no. 1-2, 1-3.
Research Day 2016: Research Activity
17
[3] Ellis, Graham. Cohomological periodicities of
crystallographic groups. J. Algebra 445 (2016),
537-544.
[1] On linear shift representations, Journal of Pure
and Applied Algebra 219, 3482â 3494, 2015
(with R. Egan).
[4] Ellis, Graham.
GAP package HAP: Homological Algebra Programming version
1.11.13, 03/11/2015.
http://www.gapsystem.org/Packages/hap.html
[2] Classifying cocyclic Butson Hadamard matrices, Springer Proceedings in Mathematics and
Statistics (PROMS): Algebraic Design Theory
and Hadamard Matrices, in press, 2015 (with
R. Egan and P. Ó Catháin).
Research Activities
In 2015 Dr Bui Anh Tuan completed his PhD studies under my supervision. His thesis is on “Discrete vector fields and the cohomology of certain
arithmetic and crystallographic groups”. Ms Nisreen
Alokbi started studying a PhD with me on the topic
of “groupoid methods in applied topology”. Mr Daher Freh started to work under my co-supervison on
“Cohomology operations on groups”. I also started to
co-supervise Mr Pablo Torres on “Detection of events
in Twitter”.
I started joint research on classification of knotted
graphs with Dr Vitaliy Kurlin (Durham) and Dr
Vanessa Robbins (Canberra).
I gave talks at conferences in Jena (February), Hannover (May), Belfast (September). I continued editorial work for the three journals HHA, JHRS and
AAECC and the GAP Council.
Flannery, Dane
Current Research Interests
Active in two main fields: linear groups (especially
computational aspects), and algebraic design theory.
Continuing to expand the new area of computing
with infinite matrix groups. This encompasses the
development of innovative techniques and implementation of algorithms for the study of solvable-by-finite
groups and arithmetic subgroups of linear algebraic
groups.
The book Algebraic design theory by de Launey and
Flannery describes a unifying paradigm for pairwise
combinatorial designs, of which Hadamard matrices
and their generalisations form a special case. We have
established machinery to analyse the regular subgroup structure of the automorphism group of such
designs. This forms the basis of effective solutions
to existence and classification problems for cocyclic
designs.
[3] Algorithms for arithmetic groups with the congruence subgroup property, Journal of Algebra
421, 234–259, 2015 (with A. S. Detinko and
A. Hulpke).
[4] Integrality and arithmeticity of solvable linear
groups, Journal of Symbolic Computation 68,
138–145, 2015 (with W. de Graaf and A. S.
Detinko).
Research Activities
• Invited speaker at
· Groups, Computation and Geometry,
June 9–13 2014, Colorado State University, USA;
· Algebraic Design Theory and Hadamard
Matrices, July 8–11 2014, University of
Lethbridge, Canada;
· Algorithms for Linear Groups, November
16–21 2014, Banff International Research
Station, Canada.
• Organizer, Algebraic Design Theory with
Hadamard Matrices: Applications, Current
Trends and Future Directions, Banff International Research Station, July 11–13 2014.
• Editor, Journal of the Australian Mathematical
Society.
• Irish Research Council New Foundations 2015
grant.
• Supervisor of doctoral student Ronan Egan
(Hardiman & Irish Research Council postgraduate scholarships).
• Distinguished visitor:
Professor Robert
Craigen, University of Manitoba (Algebraic
Design Theory).
• 5 papers refereed.
• 2 Mathematical Reviews.
Publications
Most significant recent publications:
Golden, Aaron
Research Day 2016: Research Activity
Current Research Interests
On leave of absence.
Publications
Research Activities
18
[4] Hinde, J (2015) All statistical models are
wrong, some are usable! In Proceedings of
the 30th International Workshop on Statistical
Modelling, Volume 1, Linz, Austria, 67–85.
Research Activities
• Graduate students: 3; Visiting Postdoc: 1
Hayes, Michael
Current Research Interests
On leave of absence.
Publications
Research Activities
Hinde, John
Current Research Interests
Statistical modelling, particularly generalized linear
models and random effects and mixture models; statistical computing and statistical software; likelihood
theory and inference; applications of statistics in biological, medical and social sciences.
• Journal submissions: 7 under review; 3 under
revision
• Conferences: Keynote 5; Invited Speaker 3;
Contributed presentations 2
• Seminar talks: 7; Public Lecture: 1
• Research Visits:
ESALQ/USP, Brazil –
July/August 2015; University of Christchurch
Canterbury – Feb/April 2016.
• Conference Organisation: Organising President, IBC2016 Vicotoria, Canada; co-chair of
Scientific Programme Committee RBras 2016,
Salvador, Brasil; member of Scientific Programme Committee IWSM 2017, Groeningen,
The Netherlands.
Publications
• Editorships: Statistics and Computing (Associate); Computational Statistics and Data
Analysis (Associate & Guest Editor); Statistical Modelling (Advisory Board); Econometrics
and Statistics (Guest Editor). Referee for numerous journals.
Journal papers: 1; Conference Papers: 5; Software 1.
Most significant recent publications
• President of the International Biometric Society
(2013-2017)
[1] Alvarez-Iglesias, A., Hinde, J., Scarrott, C. and
Newell, J. (2015) Summarising censored survival data using the mean residual life function.
Statistics in Medicine, 34(11), 1965â -1976
[2] Coffey, Norma, Hinde, John and Holian, Emma
(2014) Clustering longitudinal profiles using Psplines and mixed effects models applied to
time-course gene expression data. Computational Statistics and Data Analysis, 71, 14–29.
[3] Islam, Nahidul; Whitehouse, Michael; Mehendale, Sanchit; Hall, Michael; Tierney, Joanna;
O’Connell, Enda; Blom, Ashley; Bannister, Gordon; Ceredig, Rhodri; Hinde, John;
Bradley, Benjamin (2014) Post-traumatic
Immunosuppression is Reversed by Anticoagulated Salvaged Blood Transfusion;
Deductions from studying Immune Status after
Knee Arthroplasty. Clinical and Experimental
Immunology, 177(2), 509â -520.
Holian, Emma
Current Research Interests
Mixture modelling to cluster longitudinal data profiles and to model the group features via generalized
linear mixed models and penalized smoothing models,
leading to the formulation of the Regression Cluster
Model (RCM). Analysis into capability of the RCM
to handle missing data within profiles or profiles measured at variable time-points. Extension of the RCM
to longitudinal profiles measured on discrete or categorical scales. P-Splines and mixed effects model
clustering. Applications in microarray analysis.
Prognostic models in Breast Cancer, variable selection methods in survival models for data with various
missingness mechanisms.
Research Day 2016: Research Activity
Publications
[1] “Her-2 Breast Cancer Treatments Induced Variations in the Patterns of Survival and Metastasis in Her-2 Positive Breast Cancers” A.
McGuire, O. Kalinina, E. Holian, K. Sweeney,
C. Malone, R. McLaughlin, A. Lowery, J. A. L.
Brown, M. J. Kerin. (2015) Conference Paper
in Irish Journal of Medical Science 184:S397S397, Sept 2015
[2] “Exosome-mediated trafficking of microRNAs
by breast cancer cells. D. P. Joyce, C. L. Glynn,
J. Brown, E. Holian, P. Dockery, M. J. Kerin,
R. M. Dwyer (2015) Cancer Research 75 (9 Supplement): P4-07-05 May 2015
[3] “Investigation of exosome-encapsulated microRNAs as potential circulating biomarkers of
breast cancer.” D. P. Joyce, M. Higgins, C. L.
Glynn, J. Brown, E. Holian, P. Dockery, M. J.
Kerin, R. M. Dwyer (2015) British Journal of
Surgery, April 2015
[4] “Colorectal cancer cells actively secrete
exosome-encapsulated microRNAs which are
associated with epithelial-mesenchymal transition.” C. Clancy, J. Brown, E. Holian ,
M.R. Joyce, M.J. Kerin, R.M. Dwyer (2014)
Conference: European Journal of Surgical
Oncology (EJSO)
19
techniques from finite fields, linear algebra, combinatorics and finite groups. Last year I had been working on a problem in linear algebra, to do with enumerating the number of distinct ranks arising in twodimensional subspaces of Mn (F ). More recently I
have begun working on a problem in design theory,
with a hope to discovering some interesting designs
over non-abelian groups.
Publications
Research Activities
Krnjajic, Milovan
Current Research Interests
On leave of absence.
Publications
Research Activities
Leitner, Marianne
I joined NUIG on September 01, 2015.
Research Activities
Current Research Interests
Supervision:
Ph.D student Olga Kalinina, Prognostic models
in Breast Cancer, variable selection methods in
survival models for data with various missingness
mechanisms.
My research aims at bridging the gap between mathematics and physics in the area of quantum field theory. My previous work relates to the quantum Hall
effect in graphene like materials and features interesting number theoretical and geometrical aspects,
part of which are not yet fully explored. More recent
work is devoted to a sound mathematical formulation
of conformal field theory on Riemann surfaces of arbitrary genus, using tools from algebraic geometry.
This is a joint project with Werner Nahm (DIAS).
I recently became interested in learning about issues
related to the elliptic genus. I plan to approach the
subject within the framework of K-theory and the
corresponding Index Theory.
Memberships: Irish Statistical Association.
Affiliations: Staff member Biostatistics Unit. HRB
Clinical Research Facility, Galway, (CRFG).
Collaborative work: Statistical Consultation, Dr.
Roisin Dwyer, REMEDI, NUIG, microarray analysis
in Mesenchymal Stem Cells and Breast Cancer.
Jennings, Kevin
Current Research Interests
I am interested in difference sets, particularly those
with classical parameters. The study of these involves
Publications
“Index Theory with Applications to Mathematics and
Physics” by D.D.Bleecker and B. Booss-Bavnbek, Int.
Press of Boston 2013, 792 pp. (book review), Irish
Math. Soc. Bulletin 75 (Summer 2015), 63–70.
Research Day 2016: Research Activity
Research Activities
I accepted to supervise the Master thesis of Mr Abdullah Alharbi which would have involved some computer algebra (Abdullah left in December). I gave a
seminar talk at NUIG in October. I attended Michael
Tuite’s lecture series on VOAs. Before joining NUIG
in September, I held a postdoctoral scholarship at
DIAS. I was the main organiser of the Irish Quantum
Foundation Meeting celebrating the institute’s 75th
anniversary in May, (and the successful main applicant for an SFI workshop grant). I came to Galway
for the VOAs & MMFs conference the same month. I
attended a seminar on automorphic forms in Utrecht
and I gave a talk at DIT in April. Currently I am
a Research Associate of the School of Theoretical
Physics at DIAS.
Madden, Niall
Current Research Interests
I work in the area of numerical analysis, and, in particular, on the solution of partial differential equations by finite difference and finite element methods.
Much of my focus is on so-called singularly perturbed
problems. Solutions to these problems feature boundary and/or interior layers, and their numerical solution requires the development of quite specialised
method.
Within this area, I work in two main branches: discretizations (meaning algorithms that reduce differential equations to linear systems of equations) and
solvers (meaning algorithms that compute solutions
to these linear systems).
Publications
20
[3] Naresh M. Chadha and
An optimal time-stepping
steady advection-diffusion
Comput.
Appl.
Math.,
10.1016/j.cam.2015.07.029.
Niall Madden.
algorithm for unproblems.
J.
294:57–77, 2016.
[4] Pandelitsa Panaseti, Antri Zouvani, Niall
Madden, and Christos Xenophontos.
A
C 1 -conforming hp finite element method for
fourth order singularly perturbed boundary
value problems. Appl. Numer. Math., 104:81–
97, 2016. 10.1016/j.apnum.2016.02.002.
Research Activities
In April, I gave a research talk at the 12th Annual
Workshop on Numerical Methods for Problems with
Layer Phenomena, a two-day conference dedicated to
the 65th birthday of Hans-Görg Roos. (The 14th instance of this meeting will take place in Galway in
April 2017!) In June, I gave a talk at the 26th Biennial Numerical Analysis Conference, Strathclyde,
where I also organised a mini-symposium on singularly perturbed differential equations. I gave invited
seminars in the University of Limerick, in March, and
University College Dublin in December.
During 2015, I worked with three research students:
Thái Anh Nhan, who defended his thesis in September, Stephen Russell, who is preparing the final draft
of his thesis, and Faiza Alssaedi, who started in
February.
I refereed papers for several international journals
during 2015, including the Journal of Scientific Computing, Journal of Applied Mathematics & Computation, Applied Numerical Mathematics, Journal of
Mathematical Modelling and Analysis, Journal of
Difference Equations and Applications, Journal of
Computer Mathematics, and Numerical Algorithms.
Three publications appearing in calender year 2015.
Most significant recent publications
[1] James Adler, Scott MacLachlan, and Niall
Madden. A first-order system Petrov-Galerkin
discretization for a reaction-diffusion problem
on a fitted mesh. IMA Journal of Numerical
Analysis, 2015. 10.1093/imanum/drv045.
[2] Niall Madden and Stephen Russell. A multiscale sparse grid finite element method for a
two-dimensional singularly perturbed reactiondiffusion problem.
Adv. Comput. Math.,
41(6):987–1014, 2015.
McCluskey, Aisling
Current Research Interests
My research interests reside primarily within analytic
topology, with a particular fascination in how order
theoretic structures mesh with topology. Other ongoing research concerns continua theory in the context
of both a natural associated order (a notion of ”betweenness”), and of discrete dynamical systems.
Additionally, my research interests encompass research in undergraduate mathematics education.
Specifically, I am interested in the development
of and facility with proof and proving in abstract
Research Day 2016: Research Activity
analysis-based mathematical subjects typically taken
in mathematics-major degree programmes.
Publications
Number of publications appearing in calendar year
2015: 2
Most significant publications
[1] A. McCluskey and B. McMaster, ”Undergraduate topology: a working textbook”, Oxford University Press, 2014.
[2] J. L. Bruno and A. E. McCluskey, ”Topologies as points within a Stone space: lattice theory meets topology”, Topology Appl. 160 (2)
(2013), 273 - 279.
Research Activities
Publications: 2 published; 1 submitted.
Graduate students: Daron Anderson PhD; Michelle
Duane graduated with MSc by research in November
2015.
Conferences: Host of 18th Galway Topology Colloquium at NUI Galway in June 2015.
Host of the international 30th Summer Conference
in Topology and Its Applications at NUI Galway in
June 2015.
Member of International Steering Committee of
DELTA 2015
Research funding: 10,000 euros awarded by SFI
Conferences and Workshops programme; 2100 euros
from FÃπilte Ireland; 300 euros from IMS; 0 euros
from IRC New Foundations.
Research visitors: S. Greenwood, Auckland, May
2015 (5 weeks); John Grant McLoughlin, Canada,
September - November 2015 (6 weeks); I. Weiss,
University of South Pacific, June 2015 (4 days).
Reviewer of papers submitted to Topology and its
Applications and International Journal of Research
in Undergraduate Mathematics Education.
21
Publications
Number of publications appearing in calender year
2015: 2
Most significant recent publications
[1] “Generic quantum walks with memory on regular graphs”, Li, D., Mc Gettrick, M., Gao, F.,
Xu, J., and Wen, Q-Y., accepted in Phys. Rev.
A (2016)
[2] “Quantum walks on two kinds of twodimensional models”, Li, D., Mc Gettrick,
M., Zhang, W-W., Zhang, K-J. International
Journal of Theoretical Physics Volume: 54
Issue: 8 pp 2771-2783 (2015)
[3] “One-dimensional lazy quantum walks and occupancy rate”, Li, D., Mc Gettrick, M., Zhang,
W-W., Zhang, K-J. Chinese Physics B Volume: 24 Issue: 5 (2015)
Research Activities
I gave an invited lecture on “Quantum walks” at
the George Boole Mathematical Sciences Conference
(GBMSC) in UCC, August 2015. I refereed a number
of papers on quantum walks. In May 2015 I participated in the conference TQC2015 (Theory of Quantum Computation, Communication and Cryptography) in Brussels. I am a member of both the Irish
and American Mathematical Societies.
Meere, Meere
Current Research Interests
Analysis of reaction diffusion models describing drug
release from affinity hydrogels. Modelling drug release from novel drug eluting stents. Modelling endocytosis and the mechanics of membranes. Modelling diffusion in crystalline solids. Modelling polymer degradation.
Publications
Mc Gettrick, Michael
Current Research Interests
Quantum information and quantum computation: In
particular quantum algorithm design, quantum walks
and quantum games. Computer algebra.
Five papers in peer reviewed journals in 2015.
Most significant recent publications
[1] Sean McGinty, Tuoi T.N. Vo, Martin Meere,
Sean McKee & Christopher McCormick, Some
design considerations for polymer-free drugeluting stents: a mathematical approach, Acta
Biomaterialia, doi:10.1016/j.actbio.2015.02.006
(2015)
Research Day 2016: Research Activity
[2] Tuoi T.N. Vo & M.G. Meere, A mathematical
model for the release of peptide-binding drugs
from affinity hydrogels, Cellular and Molecular
Bioengineering, doi:10.1007/s12195-014-0375-2
(2015)
[3] O. Gladkovskaya, P. Greaney, Y. K. Gun’ko,
G. M. O’Connor, M. Meere & Y. Rochev,
An experimental and theoretical assessment
of quantum dot cytotoxicity, Toxicology,
doi:10.1039/c5tx00149h (2015)
[4] Tuoi T.N. Vo & M.G. Meere, The mathematical modelling of affinity-based drug delivery systems, Journal of Coupled Systems and Multiscale Dynamics, 3, 5 - 22 (2015)
Research Activities
Two PhD students, one co-supervised by Dr Giuseppe
Zurlo, and another co-supervised by Dr Tuoi Vo. Reviewed two papers. Mentor at the Student Modelling
Workshop, MACSI. Mentor at the Stokes Modelling
Workshop, NUIG. Delivered invited talk to CMALS,
the University of Glasgow. One week research visit
to the University of Strathclyde, December 2015.
22
markers. Journal of Sports Sciences, 33:6, 568569.
[3] Murphy AW, Cupples ME, Murphy E, Newell
J, Scarrott C, Vellinga A, Gillespie P, Byrne
M, Smith SM (2015) ’Six-year follow-up of the
SPHERE RCT: secondary prevention of heart
disease in general practice’. BMJ Open.
[4] Healy, D, Clarke-Moloney, M, Gaughan, B,
O’Daly, S, Hausenloy, D, Sharif, F, Newell, J,
O’Donnell, M, Grace, P, Forbes, JF, Cullen,
W, Kavanagh, E, Burke, P, Cross, S, Dowdall, J, McMonagle, M, Fulton, G, Manning,
BJ, Kheirelseid, EAH, Leahy, A, Moneley, D,
Naughton, P, Boyle, E, McHugh, S, Madhaven,
P, O’Neill, S, Martin, Z, Courtney, D, Tubassam, M, Sultan, S, McCartan, D, Medani,
M, Walsh, S (2015) ’Preconditioning Shields
Against Vascular Events in Surgery (SAVES),
a multicentre feasibility trial of preconditioning against adverse events in major vascular
surgery: study protocol for a randomised control trial’. Trials, 16.
Research Activities
• Current research grants: PI (1), Co-PI (1), Collaborator (3), Co-Applicant (7).
Newell, John
Current Research Interests
My primary areas of research in Biostatistics are in
the theory and application of statistical methods in
clinical trials of health service and population health
interventions and in the development of novel analytic approaches in Sports and Exercise Science. My
research interests include statistical modelling, statistical computing, design and analysis of cluster randomised trials, smoothing techniques and derivative
estimation, survival analysis, tree based classification
problems and sports analytics.
Publications
• Number of graduate students: 6
• Journal submissions: 7
• Conferences: 2
• Visits: 4
• Invited talks: 2
• Research visits: 4
• Memberships: International Society for Clinical
Biostatistics, Irish Statistical Association
• External posts: Adjunct Senior Research Fellow
in the Department of Mathematics and Statistics, University of Canterbury, Christchurch,
New Zealand.
4 publications appeared in calendar year 2015
Most significant recent publications
[1] Alvarez-Iglesias, A., Newell, J., Scarrott, C. and
Hinde, J. (2015), Summarising censored survival data using the mean residual life function.
Statistics in Medicine, 34: 1965â 1976.
[2] Newell, J., Korir, P., Moore, B., Pedlar, C.
(2015) App for the calculation of blood lactate
Ó Broin, Pilib
Current Research Interests
My research interests are focused in two main areas:
algorithm development and high-performance computing for the analysis of next-generation sequencing
data, and statistical machine learning for the identification of biomarker signatures in clinical data.
Research Day 2016: Research Activity
23
Publications
Publications
Most significant recent publications:
Most significant recent publications
[1] Tomohisa
Takahashi* ,
Shota
Okabe* ,
*
Pilib Ó Broin , Akira Nishi, Kenny Ye,
Michael Beckert, Takeshi Izumi, Hiroaki
Machida, Gina Kang, Jose L. Pena, Aaron
Golden, Takefumi Kikusui, Noboru Hiroi.
‘Structure and function of neonatal social
communication in a genetic mouse model of
autism spectrum disorders’. Mol. Psych. (in
press)
[2] Pilib Ó Broin, Terry Smith, and Aaron
Golden. ‘Alignment-free clustering of transcription factor binding motifs using a genetick-medoids approach’. BMC Bioinformatics.
16(1):22 (2015)
[3] Pilib Ó Broin, Bhavapriya Vaitheesvaran,
Subhrajit Saha, Kirsten Hartil, Emily I.
Chen, Devorah Goldman, William Harv Fleming, Irwin J. Kurland, Chandan Guha, and
Aaron Golden. ‘Intestinal Microbiota-Derived
Metabolomic Blood Plasma Markers for Prior
Radiation Injury’. Int. J. Radiat. Oncol. Biol.
Phys. 91(2):360-367 (2015)
[4] Behnam Nabet, Pilib Ó Broin, Jaime M.
Reyes, Kevin Shieh, Charles Y. Lin, Christine
M. Will, Relja Popovic, Teresa Ezponda, James
E. Bradner, Aaron A. Golden, and Jonathan D.
Licht. ‘Deregulation of the Ras-Erk signaling
axis modulates the enhancer landscape’. Cell
reports 12(8):1300-1313 (2015)
[1] 1. On abstract differential equations with non
instantaneous impulses (with E. Hernandez and
M. Pierri), Topological Methods in Nonlinear
Analysis, 46(2015), 1067–1088.
[2] 2. Asymptotic behavior of a three species
eco-epidemiological model perturbed by white
noise (with Q. Zhang, D. Jiang and Z. Liu),
Journal of Mathematical Analysis and Applications, 433(2016), 121–148.
[3] 3. Existence results for a Neumann problem
involving the p(x)–Laplacian with discontinuous nonlinearities (with G. Barletta and A.
Chinni), Nonlinear Analysis Series B: Real
World Applications, 27(2016), 312–325.
[4] 4. Weak solutions for fractional differential
equations in nonreflexive Banach spaces via
Riemann-Pettis integrals (with R.P. Agarwal,
V. Lupulescu and G. ur Rahman), Mathematische Nachrichten, 289(2016), 395–409.
Research Activities
Park, Sejong
Research Activities
Current Research Interests
Published manuscripts:6
Conference presentations:8
Invited talks:1
Graduate Students:1 PhD (co-supervised)
Professional Memberships: NYAS, ISCB, VIBE
My research topics involve representation theory finite groups and its connection with group theory and
algebraic topology. Specifically, I am working on fusion systems and related homological algebra, including cohomology of groups, and more generally, derived limits of functors over categories, Mackey functors and biset functors.
O’Regan, Donal
Current Research Interests
Nonlinear functional analysis (theory, methods and
applications).
Publications
Most significant recent publications
[1] Mislin’s theorem for fusion systems via Mackey
functors, Comm. Algebra, to appear
[2] Realizing fusion systems inside finit groups,
Proc. Amer. Math. Soc., to appear
Research Day 2016: Research Activity
24
[3] Mackey functors and sharpness for fusion systems, Homology, Homotopy Appl. 17 (2015),
no. 1, 147–164 (joint with Antonio Dı́az)
[4] Counting conjugacy classes of cyclic subgroups
for fusion systems, J. Group Theory 17 (2014),
no. 4, 661–666
Research Activities
• Research grant: Ulysses 2014 (as a project
leader, with Goetz Pfeiffer and Brendan Masterson)
• Published paper: 1
• Submitted papers: 2
• Invited talks: 2
[1] Cohomology of fusion systems, Groups and
geometries, Banff, Canada, 4â -8 May
2015
[2] Biset functors and fusion systems, Functorial Methods in Representation Theory,
EPFL, Switzerland, 1-â 4 Sep 2015
• Other talks: 6
• Conference participation: 4
[1] Representations of Finite Groups, Oberwolfach, Germany, 6–10 Apr 2015
[2] Groups and geometries, Banff, Canada, 4–
8 May 2015
[3] Groups, Representations, and Cohomology, Isle of Skye, UK, 23–26 Jun 2015
[4] Functorial Methods in Representation
Theory, EPFL, Switzerland, 1–4 Sep 2015
• Research visits
[1] Université de Picardie, Amiens, France,
19â -25 Apr 2015
[2] Universidad de Málaga, Spain, 8-â
July 2015
[3] Universitat Autònoma
Spain, 14–17 Oct 2015
• Visitors: 5
• Papers refereed: 2
O’Shea, James
de
15
Barcelona,
Current Research Interests
I am interested in a number of questions within
quadratic form theory. Most fundamentally, I am interested in understanding the isotropy behaviour of
forms with respect to extensions of their ground field,
addressing questions in the following vein: if a given
polynomial (homogeneous of degree two) attains a
root over a field extension, what other polynomials
(homogeneous of degree two) attain a root over this
field extension in consequence? I am currently investigating the isotropy of forms over function fields
of conics, an important class of field extensions. I
am also seeking to clarify the nature of the relationship that exists between the classes of “round” and
“group” forms. I am also interested in topics in Linear Algebra, and am considering questions concerning
the rank of matrices over finite fields.
Publications
Most significant recent publications
[1] Multiples of Pfister forms, Journal of Algebra
449, 214-236 (2016).
[2] The weak isotropy of quadratic forms over field
extensions, Manuscripta Mathematica 145, 143161 (2014).
[3] Isotropy over function fields of Pfister forms,
Journal of Algebra 361, 23-36 (2012).
[4] Sums of squares in certain quaternion and octonion algebras, C. R. Acad. Sci. Paris, Sér. I
349, 239-242 (2011).
Research Activities
I am currently supervising one student in the preparation of her M.Sc. thesis. I have given talks at both
the School Seminar and the Linear Algebra Seminar within the School. I am currently a committee
member of the Irish Mathematical Society, and thus
attend the Society’s scientific and general meetings.
I look forward to attending one or more of the upcoming algebra conferences that will be held in Lens,
Ghent and Telč this summer. I recently refereed an
article on the Hurwitz problem in quaternion algebras.
Pfeiffer, Götz
Research Day 2016: Research Activity
Current Research Interests
25
Research Activities
Computational algebra, representations of finite
groups and associative algebras, combinatorics and
geometry of finite Coxeter groups.
• Post-doc researcher in a joined project (“An
analysis of the opportunities for creative reasoning in undergraduate Calculus courses”) funded
by 3U NStep .
Publications
• Organiser of the 10th Annual Irish Workshop
on Mathematics Learning and Support Centres
(May27th in NUI Galway).
Most significant recent publications
[1] (with Marcus Bishop, J. Matthew Douglass and
Gerhard Röhrle) Computations for Coxeter arrangements and Solomon’s descent algebra III:
Groups of rank seven and eight, J. Algebra 423
(2015), 1213–1232.
[2] (with J. Matthew Douglass and Gerhard
Röhrle) Cohomology of Coxeter Arrangements
and Solomon’s Descent Algebra, Trans. Amer.
Math. Soc. 366 (2014), no. 10, 5379–5407.
Research Activities
Research grants: IRC Ulysses Grant (with S. Park);
Numbers of graduate students: 1; Journal submissions: 2; Conferences: 2; Invited talks: 2; Research
visits: 2; Papers refereed: 5; Math review: 4; Editorships: Mathematical Proceeedings of the Royal Irish
Academy; Memberships: Irish Mathematical Society,
American Mathematical Society;
• Committee member of the Irish Mathematics
Learning Support Network (IMLSN).
Piiroinen, Petri T
Current Research Interests
My main research interests are in the area of discontinuous dynamical systems with application to
rigid-body mechanics, evolving networks, population
dynamics, economics, psychology and biological systems. An overarching aim of my research is to bridge
the gap between mathematics and numerical analysis on one hand and biology, engineering and social
sciences on the other to make mathematical theories
more applicable to non-theoreticians.
Publications
Most significant publications
Pfeiffer, Kirsten
Current Research Interests
Publications
Most significant recent publications
[1] Sinead Breen, Ann O’Shea, Kirsten Pfeiffer
(2016) ’Students’ views of example generation
tasks’. In: Teaching Mathematics and its Applications.
[2] Pfeiffer, K. and Quinlan R. (2015) ProofEvaluation as a Step towards Proof Authorship.
In: MAA Notes. Volume ‘Beyond Lecture:
Techniques to Improve Student Proof-Writing
Across the Curriculum’.
[3] Pfeiffer, K. and Quinlan R. Proof evaluation
tasks as tools for teaching? Proceedings of the
Ninth Congress of the European Society for Research in Mathematics Education (CERME 9).
February 4th - 8st 2015, Prague (Czech Republic).
• Burns, S. and Piiroinen P.T., A hybrid scheme
for simulation of planar rigid bodies with impacts and friction using impact mappings, International Journal of Non-Linear Mechanics 77, pp. 312–324, December 2015. (DOI:
10.1016/j.ijnonlinmec.2015.09.011)
• Doherty, K., Meere, M. and Piiroinen, P.T.,
Some Mathematical Models of Intermolecular
Autophosphorylation, Journal of Theoretical Biology 370, pp. 27–38, April 2015.
(DOI: 10.1016/j.jtbi.2015.01.015)
• Donohue, J.G. and Piiroinen, P.T., Mathematical modelling of seasonal migration with applications to climate change, Ecological Modelling
299, pp. 79–94, March 2015.
(DOI: 10.1016/j.ecolmodel.2014.12.003)
Research Activities
During 2015 I supervised 4 PhD students and 1 MSc
student. The MSc student and two of the PhD students graduated. During the year I visited researchers
Research Day 2016: Research Activity
26
in Sao Paulo (Brazil), Naples (Italy) and Bangalore
(India).
Quinlan, Rachel
Current Research Interests
Linear algebra and its interactions with combinatorics, graph theory, field theory and the representation theory of finite groups. Specific current projects
involve completion problems for partial matrices and
entry pattern matrices, as well as classifications of
nilpotent spaces in positive characteristic. I also have
interests in university mathematics education.
Publications
Most significant recent publications
[1] Kirsten Pfeiffer and Rachel Quinlan. Proof
evaluation tasks as tools for teaching? Proceedings of the Ninth Congress of the European Society for Research in Mathematics Education.
pp178-184 (2015) ¡hal-01281065¿
[2] J. McTigue and R. Quinlan. Partial matrices
of constant rank, Linear Algebra and its Applications, Vol. 446, 177–191 (2014).
Röver, Claas
Current Research Interests
On leave of absence.
Publications
Research Activities
Ryan, Ray
Current Research Interests
Publications
Most significant recent publications
[1] ”Introduction to tensor products of Banach
spaces”, Springer Monographs in Mathematics,
Springer-Verlag, London, 2002.
[2] with C. Boyd, ”Geometric theory of spaces
of integral polynomials and symmetric tensor
products”, J. Functional Analysis 179 (2001),
no. 1, 18–42.
[3] J. Cruickshank, A. Herman, R. Quinlan, F.
Szechtman, Unitary groups over local rings,
Journal of Algebra and its Applications, Vol.
13, Issue 02 (2014)
[3] with B. Grecu, ”Polynomials on Banach spaces with unconditional bases”,
Proc. Amer. Math. Soc 133 (2005), no. 4,
1083–1091.
[4] J. McTigue and R. Quinlan, Partial matrices
whose completions all have the same rank, Linear Algebra and its Applications, Vol 438, no.
1, pages 348–360 (2013)
[4] with C. Boyd, ”The norm of the product of
polynomials in infinite dimensions”, Proc. Edinburgh Math. Soc. (2) 49 (2006), no. 1, 17–28.
Research Activities
I am currently supervising the PhD research of two
students, Olga O’Mahony and Ha Van Hieu. I was
also the supervisor of James McTigue who completed his PhD in 2015. I am the coordinator of the
weekly linear algebra seminar which ran throughout
Semester 2 this year. In 2015 I gave research presentations at the Ninth Congress of the European Society
for Research in Mathematics Education in Prague,
and in the UCD Algebra seminar (as well as locally).
In Summer 2015 I supervised the Summer internsip
of Cian O’Brien. I have recently refereed articles for
the Journal of Algebra and for Linear Algebra and its
Applications and reviewed three articles for Mathematical Reviews in 2015. I am the author of one book
review in the Bulletin of the IMS in 2015.
Research Activities
• “Polynomial and Holomorphic Mappings on
Riesz Spaces”, minicourse at 11th ILJU School
of Mathematics, Gyeongju, Korea, September
2016.
• “Free and Projective Vector Lattices”, Dublin
Analysis Seminar, UCD, June 2015.
• ”Regular Holomorphic Functions on Complex
Banach Lattices”, Workshop on Infinite Dimensional Analysis, Buenos Aires, July 2014.
Rahm, Alexander D.
Started a postdoctoral fellowship at the University of
Luxembourg on 1 September 2015.
Research Day 2016: Research Activity
Current Research Interests
Algebra, Geometry & Topology, e.g. homology of
arithmetic groups, isometries of hyperbolic space.
Publications
Most significant recent publications:
[1] Alexander D. Rahm and Matthias Wendt, A
refinement of a conjecture of Quillen. Comptes
Rendus Mathématique (2015)
[2] Alexander D. Rahm, Complexifiable characteristic classes. Journal of Homotopy and Related
Structures (2014)
[3] Alexander D. Rahm, Accessing the cohomology
of discrete groups above their virtual cohomological dimension. Journal Of Algebra (2014)
[4] Alexander D. Rahm, The homological torsion
of PSL2 of the imaginary quadratic integers.
Transactions of the American Mathematical Society (2013)
Research Activities
Grants: ICHEC grant of 900,000 processor hours
(value: 30,000 Euro); IHÉS grant for one-month
funded research stay; MFO grant for two-weeks
funded research collaboration stay at Oberwolfach,
joint with Rob de Jeu, Herbert Gangl and Dan
Yasaki. PhD student: Daher Al-Baydli (jointly supervised with Emil Skoldberg); Master student: Katherine Wilkie. Papers in progress: Manuscripts with
Matthias Wendt, resp. Ethan Berkove submitted
to journals; preprint with Rob de Jeu; preprint on
orbifolds which is under completion joint with Fabio
Perroni. Talks: 3 international conference/workshop
contributions in 2014 (3 confirmed so far in 2015), 2
invited seminar talks in 2014 (3 confirmed so far in
2015). Papers refereed for Mathematische Annalen,
Journal fà r die reine und angewandte Mathematik
(Crelle’s Journal), Journal of Pure and Applied Algebra (JPAA), Homology, Homotopy and Applications
(HHA), Discrete & Computational Geometry. Editorial board member of Research Matters, NUI Galway.
Member of IMS, EMS, SMF and DMV.
Seoighe, Cathal
Current Research Interests
My research interests are in several areas of bioinformatics/computational biology: Genomics and epi-
27
genetics, including gene expression deconvolution,
mRNA splicing and analysis of chromatin structure
using high throughput sequencing data; development
and application of probabilistic models of evolution;
genetic variation in human molecular phenotypes, including gene expression, splicing and mutation rates;
computational immunology, including tools for analysis of immune receptor diversity. Bioinformatics is
interdisciplinary and I collaborate with several other
research groups on campus. A major focus of recent
collaborations involves the analysis of data from high
throughput sequencing technologies. These technologies can be used to sequence genomes or for studying
gene expression or the binding of proteins to DNA.
Publications
4 journal articles appeared in 2015.
Most significant recent publications
[1] LymAnalyzer: a tool for comprehensive analysis of next generation sequencing data of T cell
receptors and immunoglobulins. Yu Y, Ceredig
R, Seoighe C. Nucleic Acids Res. 2016 Feb
29;44(4)
[2] Promiscuous mRNA splicing under the control
of AIRE in medullary thymic epithelial cells.
Keane P, Ceredig R, Seoighe C. Bioinformatics.
2015 Apr 1;31(7):986-9
[3] Seq-ing improved gene expression estimates
from microarrays using machine learning. Korir
PK, Geeleher P, Seoighe C. BMC Bioinformatics. 2015 Sep 4;16:286.
[4] Population genetics inference for longitudinallysampled mutants under strong selection.
Lacerda M, Seoighe C. Genetics.
2014
Nov;198(3):1237-50.
Research Activities
My research group consisted of six PhD students in
2015. Current research grants are from the EU (Marie
Sklodowska Curie), IRC, Science Without Borders
(Brazil), PRTLI (through the graduate programme in
simulation science) and SFI (H2020 Catalyst Award).
Academic community service included membership of
the editorial board of Briefings in Bioinformatics, review of grants for the Natural Sciences and Engineering Research Council of Canada and refereeing for a
range of journals. Member of the International Society for Computational Biology. Gave a keynote talk
at ISMB satellite meeting for Integrative RNA Biology.
Research Day 2016: Research Activity
Sheahan, Jerome
Current Research Interests
Sequences of various kinds, including iid and dependent sequences.
Publications
Three research publications
Research Activities
Sköldberg, Emil
Current Research Interests
28
[1] G. Mason and M.P. Tuite, Free bosonic vertex operator algebras on genus two Riemann
surfaces II. â
Conformal Field Theory, Automorphic Forms and Related Topicsâ , Contributions in Mathematical and Computational
Sciences 8 183-225, (Springer Verlag), (2014).
[2] M.P. Tuite and Hoang Dinh Van, On exceptional vertex operator (super) algebras, ”Developments and Retrospectives in Lie Theoryâ ,
Developments in Mathematics Volume 38 351384 (Springer Verlag) (2014).
Research Activities
[1] Invited talks at University of Cologne, a workshop on Mathieu Moonshine Durham University and a VOA conference in Chengdu China.
[2] 1 PhD student with IRC funding
[3] 2 journal submissions
I work on combinatorial commutative (and noncommutative) algebra. In particular, I am interested
in homological properties of such algebraic structures,
recently in particular the study of the existence of
differential graded algebra structures on minimal resolutions of certain classes of monomial ideals in the
commutative polynomial ring.
Current Research Interests
Publications
Publications
Research Activities
Research Activities
Ward, James
Algebra, Subnormal Subgroups, History of Mathematics.
Yang, Haixuan
Tuite, Michael
Current Research Interests
Current Research Interests
Vertex operator algebras (VOAs), conformal field theory, Riemann surfaces, elliptic, Jacobi and modular
functions in number theory and combinatorics. In
the past year I completed a major paper with Tom
Gilroy where we describe a genus two version of Zhu
theory for VOAs. I am also working on the solution
of a partial differential equation describing all genus
two partition functions for the (2,5) minimal model
VOA with Tom Gilroy at UCD, quasi-Jacobi forms
in VOAs with Kathrin Bringman and Matt Krauel of
University of Cologne and on VOA book collaboration with .Geoff Mason at UC Santa Cruz
My focus is in Bioinformatics & Statistical Modelling,
especially of network data such as protein-protein interactions, co-expression, and functional similarity.
A bio-molecular network can be viewed as a collection of nodes, representing the bio-molecules, connected by links, representing relations between the
bio-molecules. I am working on inferring valuable information from bio-molecular networks.
Publications
Most significant recent publications
Publications
Most significant recent publications
[1] Y Jiang et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. arXiv, 2016.
Research Day 2016: Research Activity
[2] SP Smieszek, H Yang, A Paccanaro, PF Devlin. Progressive promoter element combinations classify conserved orthogonal plant circadian gene expression modules. Journal of The
Royal Society Interface 11 (99), 2014.
[3] P Radivojac et al. A large-scale evaluation of
computational protein function prediction. Nature Methods 10 (3), 2013.
Research Activities
Presented the work ”A Graph-based Logistic Regression Model and Its Application to Protein Function
Prediction” in CASI2015. Presented the work ”A
post-processing method of NMF for molecular cancer
subtype discovery” in VIBE2015. Visited TsingHua
University. Refereed papers for ”IEEE Transactions
on Neural Networks and Learning Systems”, ”Gene”,
and ”Bioinformatics”.
Zurlo, Giuseppe
Current Research Interests
I am deeply interested in those phenomena that can
be modeled by Continuum Mechanics and Thermodynamics. My research is focused on the modeling of
material behavior at the intersection of Continuum
Mechanics with Biology, Medicine and Electromagnetism. More in detail, I work on the theory of growth
in biological materials, on the mechanical behavior of
cell membranes, with recent emphasis on endocytosis,
on finite plasticity theory, on the theory of finite elasticity with a specific focus on the mechanics of thin
bodies, on the electromechanics of highly deformable
materials.
Publications
Most significant recent publications
[1] S Colonnelli, G Saccomandi, G Zurlo, The role
of material behavior in the performances of electroactive polymer energy harvesters Journal of
Polymer Science Part B: Polymer Physics 53
(18), 1303-1314
Research Activities
[1] invited
talk
to
the
Mathematisches
Forschungsinstitut Oberwolfach (MFO, Oberwolfach Research Institute for Mathematics)
November 2015
29
[2] co-supervisor (with Dr Martin Meere) of 1 PhD
thesis (student: Paul Greaney)
[3] 3 journal submissions
[4] research visits in Ecole Polytechnique, Institut
Curie (Paris), Universit a di Perugia, Politecnico di Bari
[5] reviewer for various scientific journals (Proceedings of the Royal Society A, Journal of Elasticity, Journal of Physics D, ... )
[6] member of the Italian group of Mathematical
Physics (GNFM)
Visitors
Murphy, Jerry
Dates of visit: 10-11 May 2015 Dr Murphy is Lecturer
in Mechanical Engineering at DCU and Adjunct Lecturer in the School of Mathematics, Statistics and
Applied Mathematics. He visited Professor Michel
Destrade to work on the mechanical behaviour of fibrous soft matter.
Research Interests
A complete treatment of the problem of Dominant
negative Poynting effect for soft tissues, published in
Journal of Engineering Mathematics [95 (2015) 87-98]
Saccomandi, Giuseppe
Dates of visit: 14-17 August 2015 Professore Saccomandi is Professor in Mechanical Engineering at
the Universita di Perugia and Adjunct Professor in
the School of Mathematics, Statistics and Applied
Mathematics. He visited Professor Michel Destrade
to work on the mechanical behaviour of rubbers.
Research Interests
A complete treatment of the problem of Methodical
Fitting for Mathematical Models of Rubber-like Materials, under review.
Lusetti, Irene
Research Day 2016: Research Activity
Dates of visit: 01-31 August 2015 Ms Lusetti is a Masters Student in Mathematical Engineering at Politecnico di Milano. She visited Professor Michel Destrade
to work on the mechanical stability of soft matter,
with support from the College of Science.
Research Interests
A complete treatment of the problem of Stability of
bent layered solids, in preparation.
30
Research Interests
A complete proposal submitted to the European
Commission for a Marie Curie Initial Training Network.
Visiots to Sejong Park
Dates of visit:
[1] 21–28 Apr 2015: Serge Bouc, Radu Stancu
[2] 29 Sep – 4 Oct: Antonio Dı́az
Su, Yipin
Dates of visit: 01 November 2015-02 April 2016 Mr
Su is a PhD Student in Mechanical Engineering at
Zhejiang University. He visited Professor Michel Destrade to work on the mechanical behaviour of electroactive soft solids, with support from his university.
Research Interests
[3] 29 Sep – 2 Oct: Radu Stancu
[4] 6–10 Oct 2015: Hiroyuki Nakaoka
Research Interests
[1] Representation theory of finite groups
[2] Fusion systems and related homological algebra
[3] Biset functors (Mackey functors)
A complete treatment of the problem of Stability soft
dielectrics for half-spaces and plates, two articles in
preparation.
I am collaborating with Goetz Pfeiffer on biset functors, in particular the structure of the double Burnside ring B(G, G) of a finite group G.
Carfagna, Melania
MacLachlan, Scott, Memorial University of
Newfoundland
Dates of visit: 15 November 2015-15 February 2016
Ms Carfagna is a PhD Student in Mathematica Engineering at Politecnico di Torino. She visited Professor
Michel Destrade to work on the the stability of soft
solids, with support from her university.
Research Interests
A complete treatment of the problem of oblique wrinkles for half-spaces and layered substrates, under review.
Dates of visit: 22–19 April.
Research Interests
Scott worked with Niall on completing revisions to a
paper on a least-squares finite element method, and
with Thái and Niall on a multigrid preconditioner
for reaction-diffusion problems in one and two dimensions. He also gave a seminar to the SIAM Chapter.
Linß, Torsten, FernUniversität in Hagen
Balbi, Valentina
Dates of visit: 12 November 2015-12 January 2016
Ms Balbi is a Post-doctoral fellow at the Universite
Pierre et Marie Curie. She visited Professor Michel
Destrade to prepare a grant proposal, with support
from Enterprise Ireland.
Dates of visit: 30 November – 1 December.
Research Interests
Torsten worked with Niall on long-running project
involving the analysis of a time-stepping alternatingdirection method.
Miszczak, Jarek
Dates of visit: 9/11/2015 to 13/11/2015
Research Day 2016: Research Activity
Research Interests
Dr. Miszczak visited NUI, Galway to carry out research with Dr. M. Mc Gettrick on quantum walks
and quantum evolutionary game theory: He gave a
seminar on “Why quantum mechanics is (not) special”
31
Research Day 2016: Research Activity
Postgraduate Students
• Daher Al-Baydli daher.mathematics@gmail.com
• Faiza Alssaedi f.alssaedi1@nuigalway.ie
• Daron Anderson d.anderson2@nuigalway.ie
• Alan Barnicle a.barnicle1@nuigalway.ie
• Sofia Barreira sofianbarreira@gmail.com
• Anh Tuan Bui a.bui1@nuigalway.ie
• Issac Burke i.burke1@nuigalway.ie
• Richard Burke richardburke8@gmail.com
• Shane Burns s.burns3@nuigalway.ie
• Simone Coughlan s.coughlan9@nuigalway.ie
• John Donohue j.donohue1@nuigalway.ie
• Liam Doonan liamd219@gmail.com
• Ronan Egan r.egan3@nuigalway.ie
• Lida Fallah lida fallah@yahoo.com
• Artur Gower arturgower@gmail.com
• Paul Greaney p.greaney3@nuigalway.ie
• Ha Van Hieu hieuhavan88@gmail.com
• Amirhossein Jalali a.jalali2@nuigalway.ie
• Olga Kalinina o.kalinina1@nuigalway.ie
• Peter Keane peterakeane@gmail.com
• Adib Makrooni m.makrooni1@nuigalway.ie
• Barbara Martinelli martinelli.bz@gmail.com
• Brendan Masterson b.masterson1@nuigalway.ie
• Shirin Moghaddam sh.moghaddam@alumni.ut.ac.ir
• Michael McCague michaelmccague@yahoo.com
• Ngoc Thanh Nguyen thanhngochp@gmail.com
• Anh Thai Nhan a.nhan1@nuigalway.ie
• Olga O’Mahony o.omahony1@nuigalway.ie
• Davood Roshan d.roshansangchin1@nuigalway.ie
• Stephen Russell s.russell1@nuigalway.ie
• Qays Shakir q.shakir2@nuigalway.ie
• Eoghan Staunton e.staunton2@nuigalway.ie
• Philip Vernon p.vernon2@nuigalway.ie
• Michael Welby
• Yaxuan Yu yuyaxuan0@gmail.com
32
Research Day 2016: Research Activity
Seminars
[1] Oliver Mason, Maynooth University.
The
Markov Chain Tree Theorem in the Max
Algebra and Semirings, 22/01/2015. (Contact: Niall Madden)
[2] Paul Hurley, IBM Research – Zurich. Reimagining the radio telescope and
sampling from Gaussian processes,
05/02/2015. (Contact: Jerome Sheahan)
[3] Kevin Jennings, NUIG. Some comments
on the ranks of subspaces of Mn(F),
05/03/2015. (Contact: Haixuan Yang)
[4] Baptiste Rognerud,
EPFL,
Switzerland.
Equivalences between blocks of cohomological algebras, 12/03/2015. (Contact:
Sejong Park)
[5] Tom Brady, DCU. Triangulating the permutahedron, 19/03/2015. (Contact: Emil
Skoldberg)
[6] Fabio Perroni, University of Trieste, Italy.
Topology of the moduli space of curves
with a given group of automorphisms,
26/03/2015. (Contact: Alexander Rahm)
[7] Timothy J. Healey, Cornell University, USA.
Wrinkling of Highly Stretched Elastic
Sheets, 01/04/2015.
(Contact: Giuseppe
Zurlo)
[8] Laurence Hurst, University of Bath, UK. Why
there is more to gene evolution than protein function: splicing and dual-coding
sequence, 09/04/2015.
(Contact: Cathal
Seoighe)
[9] Scott MacLachlan,
Memorial
University,
Canada. Parallel-in-time integration using multigrid, 23/04/2015. (Contact: Niall
Madden)
[10] Piotr Gawron, Polish Academy of Sciences,
Poland. Generalized open quantum walks
on Apollonian networks, 29/04/2015. (Contact: Michael Mc Gettrick)
[11] Alberto Paccanaro, Royal Holloway University
of London, UK. Inference and structure discovery in biological networks, 14/05/2015.
(Contact: Haixuan Yang)
[12] Ruben Sanchez-Garcia,
University
of
Southampton, UK. Topology and Geometry of Networks and Data, 20/05/2015.
(Contact: Alexander Rahm)
33
[13] Matthias Wendt, Universitaet Duisburg-Essen,
Germany. Buildings and K-theory of elliptic curves, 28/05/2015. (Contact: Alexander
Rahm)
[14] Sina Greenwoody, University of Auckland, New
Zealand. Generalised inverse limits and
continua, 04/06/2015. (Contact: Aisling McCluskey)
[15] Sushing Chen, University of Florida, USA. Big
Data and Precision Medicine, 12/06/2015.
(Contact: Cathal Seoighe)
[16] Nesrin Manav, Gazi University, Turkey. Fixed
Point Theorems on Modular Metric
Spaces, 03/09/2015. (Contact: Raymond
Ryan)
[17] Dessislava Kochloukova, State University of
Campinas, Brazil. Weak commutativity in
groups, 10/09/2015. (Contact: Grahamj Ellis)
[18] Javier Aramayona, Institut de Mathà matiques de Toulouse, France. The abelianization of automorphism groups of rightangled Artin groups, 17/09/2015. (Contact:
Grahamj Ellis)
[19] Neil Oâ èConnell,
Warwick
University,
UK. Increasing subsequences, Young
tableaux, and related topics, 24/09/2015.
(Contact: Raymond Ryan)
[20] Marianne Leitner, NUIG. CFT on Riemann
surfaces, 01/10/2015. (Contact: Grahamj Ellis)
[21] Hiroyuki Nakaoka, Università de Picardie /
Kagoshima University, France / Japan. Preadditive categories as a categorification of
rings; quotients, spans and their applications, 08/10/2015. (Contact: Sejong Park)
[22] John McLoughlin,
University
of
New
Brunswick, Canada. Enriching the Scope
of Mathematical Experiences with
Problems, 15/10/2015. (Contact: Aisling
McCluskey)
[23] Pilib à Broin, NUIG. The role of the
Tbx1 gene in a mouse model of autism
spectrum disorder, 22/10/2015. (Contact:
Cathal Seoighe)
[24] Antonio DÃ az, Universidad de MÃπlaga,
Spain. Simplicial complexes and Quillen’s
complexes, 29/10/2015. (Contact: Sejong
Park)
Research Day 2016: Research Activity
[25] James O’Shea, NUIG. Field Invariants and
Pfister forms, 05/11/2015. (Contact: Rachel
Quinlan)
[26] Eric Ladizinsky,
D-Wave Systems Inc.,
USA. Evolving Quantum Computers,
10/11/2015. (Contact: Michael Mc Gettrick)
[27] Jaroslaw Miszczak, Polish Academy of Science,
Poland. Why quantum mechanics is (not)
special?, 12/11/2015. (Contact: Michael Mc
Gettrick)
[28] Yoshifumi NAKATA, The University of Tokyo,
Japan. Unitary designs: constructions
and applications in quantum information
theory, 26/11/2015. (Contact: Michael Mc
Gettrick)
[29] Vitaly Kurlin, University of Durham, UK.
Computing invariants of knotted graphs
given by sequences of points in 3dimensional space, 03/12/2015. (Contact:
Grahamj Ellis)
[30] Giovanni Russo, IBM Research – Dublin.
Analysis and control of networked systems:
from biology to smart cities,
09/12/2015. (Contact: Petri Piiroinen)
[31] Miguel Bustamante, UCD. Precession Resonance and Strong Energy Transfers
in Nonlinear Wave Systems, 17/12/2015.
(Contact: Michel Destrade)
[32] Fionnuala Connolly, Harvard University, USA.
Developing Design Rules for Soft Fluidic
Actuators, 18/12/2015. (Contact: Michel Destrade & Raymond Ryan)
34
problems in pollution, drug release from polymers, aircraft wing vibration, flight networks,
and structural isomers. They were mentored
by staff and students of the Stokes Cluster for
Applied Mathematics.
• NUI Galway SIAM Student Chapter Annual
Conference 2015
Date: 3 December 2015
Invited speakers: Dr Dana Mackey (DIT) and
Prof. James Gleeson (UL)
Contributed talks: Brendan Murray (UCD),
Naoise Holohan (TCD), Niall McInerney (UL),
Martina Curran (NUI Galway), Gary O’Keeffe
(UL), Alan Compelli (DIT) Kevin Devine (UL).
Organisers:Richard Burke, Christine Marshall,
Paul Greaney, Niall Madden, Faiza Alssaedi,
Shane Burns, Stephen Russell, Bram Siebert,
Eoghan Staunton and Michael Welby
• Group in Galway
Date: 22 - 23 May 2015
Invited speakers: Nicolas Bergeron (Università de Paris 7), Serge Bouc (Università de
Picardie - Jules Verne), Hans Cuypers (Technische Universiteit Eindhoven), Tom de Medts
(Ghent University), Peter Kropholler (University of Southhampton), Goetz Pfeiffer (NUI
Galway), Radu Stancu (Università de Picardie
- Jules Verne), Alain Valette (Università de
NeuchÃÊtel).
Organisers: Sejong Park & Alexander Rahm
• ”Vertex operator algebras and mock modular
forms” workshop
Date: 22-23 May 2015
Funded by IRC and SFI.
Conferences and Workshops
• Stokes Modelling Workshop
Dates: 15–18 June, 2015
Organisers and mentors:
Shane Burns, Paul Greaney, Niall Madden,
Martin Meere, Richard Burke, Shane Burns,
Michel Desdrade, John Donohue, Michael Mc
Gettrick, Eoghan Staunton, Michael Tuite, and
Giuseppe Zurlo.
Twenty four undergraduate students from various Irish universities came to Galway for a week
to study techniques in modelling, and to solve
Speakers: Drazen Adamovic (University of Zagreb, Croatia), Nicolas Bergeron (UniversitÃ
de Paris 7, France), Thomas Creutzig (University of Alberta, Canada), Terry Gannon (University of Alberta, Canada), Matt Krauel (University of Cologne, Germany), Ching Hung Lam
(Academia Sinica, Taiwan), Sameer Murthy
(Kings College London, UK), Roberto Volpato
(SLAC and Stanford University, USA)
Nicolas Bergeron was a joint speaker with
Groups in Galway.