Homepage of Dr. Adnan Sljoka Postdoctoral Fellow Department of
Mathematics and Statistics, York University 4700 Keele Street, Toronto, ON., Canada M3J 1P3 E:mail: adnanslj@matstat.yorku.ca
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Rigidity Theory, Algorithms for modeling protein rigidity/flexibility and protein motions, Allosteric interactions in proteins, Linkage Motions and Decompositions in Mechanical engineering and robotics, Matroid Theory, Graph Theory, Computational Biology and Bioinformatics, Computational Geometry, Mathematical Biology and Mathematics Education.
Rigidity-based allosteric
communication in agonist-bound adenosine receptor, a type of GPCR.
Simulation of immunoglobulin
About me:
Recently, I obtained a PhD in Applied Mathematics. I worked with Walter Whiteley on applications of rigidity theory, which is a mix of geometry, graph theory and applied combinatorics. My research was primarily focused on the development of theory and algorithms with applications to a range of problems from protein flexibility predictions, bioinformatics and mechanical linkages - protein hinge motion predictions, computational predictions of HD-exchange, protein allostery and decompositions of linkages (Assur graphs). You can find my PhD thesis here. Since my work is highly interdisciplinary, a significant part of my work involves collaborations with other mathematicians, biochemists, computer scientists and mechanical engineers / researchers in robotics.
Lately, I've been investigating allosteric mechanisms in proteins, particularly in the important class of signalling proteins known as G-protein coupled receptors (GPCRs). Finding an allosteric mechanism of GPCRs is crucial as GPCRs are responsible for the control of most information that passes into the cell from the external environment. GPCRs play a critical role in many diseases (i.e heart disease, hypertension, cancer, asthma, diabetes, inflammation and psychological disorders) and are the most commonly targeted receptor class for medicinal therapeutics (it is estimated GPCRs are targets to more than 50% of all modern medicinal drugs). The recent discoveries of the 3-dimensional structures of some GPCRs has led to a Nobel prize in Chemistry. Recently, I've been also thinking about the impact of symmetry on protein motions.
I am also interested in mathematics education and teaching and have formal teacher training.
Besides academics, I have played competitive tennis and was part of the York University varsity tennis team for 4 years.
You can find my full CV here.
Publications:
• Shai O., Sljoka A. and Whiteley W., Directed Graphs, decompositions and Spatial Decompositions, submitted to Discrete Applied Mathematics, 2012, arXiv:1010.5552.
• Sljoka A., Algorithms in rigidity theory with applications to protein flexibility and mechanical linkages, PhD dissertation, York University, Toronto, 2012.
• Schulze B., Sljoka
A. and Whiteley W., How does symmetry impact the
flexibility of proteins?, submitted to Philosophical Transactions of Royal
Society, 2012.
• Sljoka A., Shai O. and Whiteley W., Checking Mobility and Decomposition of Linkages via Pebble Game Algorithm, Proceedings of the ASME 2011 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, IDETC/CIE 2011, August 29-31, 2011, Washington, DC, USA.
• Sljoka A. and Bezginov A., Predicting hinge motions and allostery using rigidity theory, Advances in Mathematical and Computational Methods: Addressing
Modern Challenges of Science, Technology, and Society, The International Conference on
Applied Mathematics, Modeling and Computational Science, Volume 1368, pp. 167- 170, Waterloo, Canada, 2011.
• Schulze B., Sljoka
A. and Whiteley W., Protein flexibility of dimers: Do symmetric motions play role in allosteric interactions, Advances
in Mathematical and Computational Methods: Addressing Modern Challenges of
Science, Technology, and Society, The International Conference on Applied Mathematics,
Modeling and Computational Science, Volume
1368, pp. 135-138 , Waterloo, Canada, 2011.
• Sljoka A., Counting for
Rigidity, Flexibility and Extensions via the Pebble Game Algorithm – Hinge
Predictions and other Biological Applications (2nd prize) ,
Third Canadian Student Conference on Biomedical Computing, 2008.
• Sljoka A., Counting for
Rigidity, Flexibility and Extensions via the Pebble Game Algorithm,
Master’s Thesis,
Preprints
/ In preparation:
• Sljoka A. and Wilson D., Probing Protein Ensemble Rigidity and predictions of Hydrogen-Deuterium exchange using rigidity theory and solvent accessibility, preprint, 2012.
• Sljoka A. Rigidity-based allosteric communication applied to G-protein coupled receptors, preprint, 2012.
• Vaidya N., Sammadi M., Sljoka A. and Huaxiong H., Coarse graining molecular dynamics with rigidity of hemagglutinin fusion peptides, in preparation.
• Shai O., Sljoka A. and Whiteley W., Inductive Constructions for 3-D Assur Graphs, in preparation.
Selected talks / invited conferences:
• Counting
for rigidity and flexibility - algorithms and applications to protein
flexibility and linkage decompositions, Seminar at Institut de Robòtica i Informàtica Industrial,
Barcelona, Spain, (Sept 21, 2012).
• Rigidity-based Allosteric communication, Allosteric
Regulation of Cell Signalling, Spanish National
Cancer Research Centre, Madrid, Spain, (September 17 - 19, 2012).
• Workshop on Rigidity, Fields
Institute for Research in Mathematical Sciences, Toronto, Canada, (Oct 11- 14,
2011).
• ASME 2011 International Design
Engineering Technical Conferences and Computers and Information in Engineering
Conference, IDETC/CIE 2011, Washington, DC, USA, (August 29-31, 2011).
• Predicting hinge motions and allostery using rigidity theory, AMMCS: Addressing Modern Challenges of Science,
Technology, and Society, The International Conference on Applied Mathematics,
Modeling and Computational Science, Volume
1368, pp. 167- 170, Waterloo, Canada, 2011.
• Predicting Rigidity and
Flexibility of proteins using rigidity theory (Poster), Recomb
2011, 15th Annual International Conference on Research in Computational
Molecular Biology, Vancouver, BC, (March 28, 29, 2011).
• Decomposition of Mechanisms: Assur Graphs and Algorithms, Geometry day at York, York
University, Toronto, Canada, (January, 26, 2011).
• Hands on Workshop on
Computational Biophysics, Beckman Institute, University of Illinois,
Urbana-Champaign, Illinois, (November 1-5, 2010).
• Rigidity of Frameworks and
Applications, Lancaster University, Lancaster, UK, (July 12-15, 2010).
• Predicting flexibility and
motions of proteins using rigidity theory, MITACS / CORS 2010 Annual
Conference, Edmonton, Canada, (May 25, 2010).
• Counting for rigidity and
flexibility - hinge predictions and allostery
(Poster), MITACS Annual Conference, University of New Brunswick, NB, Canada
(May 31, 2009).
• Pebble Game Algorithm, Hinge
predictions and allostery (Poster), Molecular
Simulations: Algorithms, Analysis, and Applications, Institute of Mathematics
and its Applications (IMA), University of Minnesota, Minneapolis, MN, USA (May
18, 2009).
• Pebble Game Extensions: Relevant
Regions, Hinge Motions and Allostery. Recent Progress
in Rigidity Theory, Banff International Research Station (BIRS), Banff, Canada
(July 11, 2008).
• Rigidity, Flexibility, and
Motion: Theory, Computation and Applications to Biomolecules,
Banff International Research Station (BIRS), Banff, Canada (July 6 – 11, 2008).
• Rigidity, Flexibility and Motion
in Biomolecules, Tempe, Arizona (May 14 – 18, 2006).
• Proteomics, Canadian
Bioinformatics Workshops, Université de Montréal,
Montreal (June 2005).
• Genomics, Canadian Bioinformatics
Workshops, University of Calgary, Calgary (May 2005).
• Bioinformatics, Canadian
Bioinformatics Workshops, Vancouver (February 2005).
• Discrete and Computational
Geometry Workshop at Mathematical and Scientific Research Institute (MSRI),
Berkeley, California (August 20 – 29, 2003).
Links and group
conference photos: