PhD Topic
Dynamics of Modular Evolving Complex Networks: Analysis, Control and Applications
Networks in some form underpin virtually all complex systems making their study a fundamental tool for understanding system level behaviours. Much existing work considers such networks in a static context, neglecting the fact that in many real-world systems structure changes over time, evolving due to new requirements. Do rules exist governing this process and could they be used to efficiently evolve complex networks towards specific functions, or reliably control existing systems? My PhD attempts to answer some of these questions, helping to give understanding as to how complex systems naturally arise in Nature. We are approaching this problem in two different ways. Firstly, we are using computational simulation and optimisation to explore how dynamics can be used to direct the evolutionary process, and the effects this has on resultant topologies. Secondly, we are aiming to formalise the notion of an Evolving Dynamical Network (EDN) to allow for analytical results to be derived.
Research Interests
The Fundamental Building Blocks of Complex Systems
Complex systems comprise of huge numbers of interconnected parts which current methods find difficult pull apart and analyse. Is there another way of looking at these systems that abstracts away the miniscule details and forms higher level representations at which new fundamental laws can be derived? When you look at Nature and the huge numbers of complex living systems one thing always stands out - a modular/hierarchical structure. It is my belief that although the interactions between elements may change with setting, fundamental building blocks exist that permit the predictable creation of large scale systems. My main area of interest is in attempting to find the building blocks chosen by Nature and developing methods to allow for the creation of complex systems with prescribed behaviours - "complexity engineering".
Synthetic Biology as a Tool to Understand Complex Systems
Synthetic biology is a new area of research that attempts to combine ideas from engineering and biology with the aim of allowing for the creation of fully synthetic biological systems. Within this field I am particularly interested in the creation of synthetic genetic regulatory circuits (GRNs) using Bio-Bricks as a foundation. A Bio-Brick is a piece of DNA that conforms to an agreed standard structure allowing for many of them to be pieced together using common lab techniques. What excites me the most is the possibility it opens to creating biological machines that can perform previously impossible tasks. It also provides a view into how complex biological systems can be built from the bottom up and is a useful foundation to test hypotheses relating to possible generic building blocks.
Novel Computing Architectures
With current computer processor chip manufacture reaching the limits of miniaturisation, we are seeing the increased adoption of new computing architectures, e.g. multi-core and heterogeneous computing. These aim to get around the limited speeds by utilising large numbers of processing resources all running simultaneously on the different parts of the same problem - a divide and conquer approach. Although many problems can be decomposed to make good use of this shift, highly sequential processes suffer only being able to harness a small portion of the resources available. I am interested in understanding if there are completely new computing paradigms that can be used to get around some of these problems and to allow us to express problems in new ways. This includes the incorporation of ideas from Nature and techniques from bio-engineering with the hope of building highly resilient systems that can adapt and learn using distributed control and highly parallel, asynchronous processing.
Publications and Reports
Peer-Reviewed Papers
T.E. Gorochowski, M. di Bernardo, C.S. Grierson.
Using aging to visually uncover evolutionary processes on networks. IEEE Transactions on Visualization and Computer Graphics, (Early View)
T.E. Gorochowski, M. di Bernardo, C.S. Grierson.
Evolving dynamical networks: a formalism for describing complex systems. Complexity, 17, pp. 18-25 (2012) *Featured on cover*
P. DeLellis, M. di Bernardo, T.E. Gorochowski, G. Russo.
Synchronization and Control of Complex Networks via Contraction, Adaptation and Evolution. IEEE Circuits and Systems Magazine: Special Issue on Complex Networks, 10:3, pp. 64-82 (2010) ISSN:1531-636X
T.E. Gorochowski, M. di Bernardo, C.S. Grierson.
A dynamical approach to the evolution of complex networks. Proceedings of the 19th International Symposium on Mathematical Theory of Networks and Systems, pp. 1083-1087 (2010) ISBN:978-963-311-370-7
T.E. Gorochowski, M. di Bernardo, C.S. Grierson.
Evolving enhanced topologies for the synchronization of dynamical complex networks. Physical Review E 81, p. 056212 (2010)
Other Articles
T.E. Gorochowski, M. di Bernardo, C.S. Grierson.
NetEvo: A computational framework for the evolution of dynamical complex networks. arXiv cs.MS (2009)
Project Reports
Cross-Frequency Coupling of Neuronal Oscillations During Cognition
Supervisors: Dr Rafal Bogacz, Dr Matt Jones
Bacto-Builders: Micro-scale Construction by Bacteria, a Modelling Perspective
Supervisors: Prof Mario di Bernardo, Prof Claire Grierson
Vidi: 3-Dimensional Fluid Visualisation
Supervisors: Prof Robert Kerr, Dr Alexander Tiskin
Graph Algorithm Visualisation Toolkit (GAVToolkit)
Supervisor: Prof Leslie Ann Goldberg
Awards and Prizes
Second Prize, Poster Competition
Evolution at Bath and Bristol Meeting, 2011
BioBricks Foundation SB5.0 Young Researcher Travel Award ($750)
SB5.0: the Fifth International Meeting on Synthetic Biology, 2011
2nd Runner Up, Best Food or Energy Project and Gold Medal (Instructor of BCCS-Bristol Team) [wiki, press]
International Genetically Engineered Machines Competition, November 2010
Best Poster - Computational Methods and Tools Session [PDF, press]
11th International Conference on Systems Biology, October 2010
Best Model Prize and Gold Medal (Instructor of BCCS-Bristol Team) [wiki, press]
International Genetically Engineered Machines Competition, November 2009
Best Model Prize and Bronze Medal (Student of BCCS-Bristol Team) [wiki, press]
International Genetically Engineered Machines Competition, November 2008
Presented Work
Evolutionary Insights From Motif Clustering (Poster)
Evolution at Bath and Bristol Meeting
26 September 2011 - University of Bath, UK
BSim: an agent-based tool for modeling synthetic bacterial populations (Poster)
RoSBNet Synthetic Biology Workshop
20 - 22 July 2011 - University of Oxford, UK
BSim: an agent-based tool for modeling synthetic bacterial populations (Poster)
SB5.0: Fifth International Meeting on Synthetic Biology
15 - 17 June 2011, Stanford University, California, USA
Evolving dynamical networks for synchronization: analysis and emergent properties (Talk)
SIAM Conference on Applications of Dynamical Systems
22 - 26 May 2011, Snowbird, Utah, USA
Evolving dynamical networks for synchronisation (Talk)
BAMC: British Applied Mathematics Colloquium
11 - 13 April 2011, University of Birmingham, UK
Using Ageing to Visually Uncover Evolutionary Processes on Networks (Poster and Demo)
BBSRC/AHRC Challenges of Visualising Biological Data Workshop
16 - 17 November 2010, The Grand Thistle, Bristol, UK
NetEvo - Computational Evolution of Dynamical Complex Networks (Poster)
11th International Conference on Systems Biology
10 - 15 October 2010, Edinburgh International Conference Centre, UK
NetEvo - Computational Evolution of Dynamical Complex Networks (Poster)
RoSBNet Synthetic Biology Workshop
12 - 14 July 2010 - University of Oxford, UK
A Dynamical Approach to the Evolution of Complex Networks (Talk)
19th International Symposium on Mathematical Theory of Networks and Systems
5 - 9 July 2010 - Eotvos Lorand University, Budapest, Hungary
NetEvo - Computational Evolution of Dynamical Complex Networks (Poster)
Statistical modelling and inference for networks (Statworks)
28 June - 1 July 2010 - University of Bristol, UK
Computational Evolution of Dynamical Complex Networks (Talk)
Engineering Principles in Biological Systems
14 - 16 October 2009 - Wellcome Trust Conference Centre, Hinxton, UK
NetEvo - Computational Evolution of Dynamical Complex Networks (Poster)
ECCS 09 - European Conference on Complex Systems
21 - 25 September 2009 - University of Warwick, UK
Dynamics of Complex Evolving Networks (Talk)
NetSci 09 - International Workshop and Conference on Complex Networks and their Applications
29 June - 3 July 2009 - Istituto Veneto Scienze Lettere ed Arti, Venice, Italy
Bacto-Builders (Talk)
Regional Meeting on Mathematics, Computation and Biology
2 June 2009 - University of Bristol, UK
Bacto-Builders (Talk)
iGEM Jamboree
8-9 November 2008 - MIT, USA
Bacto-Builders Modelling (Talk)
BICS Conference - Emergence in Complex Systems
9-11 September 2008 - University of Bath, UK
BCCS-Bristol iGEM Ideas (Talk)
iGEM 2008 - UK Meeting
15-16 July 2008 - University of Edinburgh, UK
Conferences and Workshops
Evolution at Bath and Bristol Meeting
26 September 2011 - University of Bath, UK
RoSBNet Synthetic Biology Workshop
20 - 22 July 2011 - University of Oxford, UK
SB5.0: Fifth International Meeting on Synthetic Biology
15 - 17 June 2011, Stanford University, California, USA
SIAM Conference on Applications of Dynamical Systems
22 - 26 May 2011, Snowbird, Utah, USA
BAMC: British Applied Mathematics Colloquium
11 - 13 April 2011 - University of Birmingham, UK
RoSBNet Meeting
12 January 2011 - Worcester College, Oxford University, UK
BBSRC/AHRC Challenges of Visualising Biological Data Workshop
16 - 17 November 2010 - The Grand Thistle, Bristol, UK
International Conference of Systems Biology 2010
10 - 15 October 2010 - Edinburgh International Conference Centre, UK
Dynamics Days Europe
6 - 10 September 2010 - University of Bristol, UK
RoSBNet Synthetic Biology Workshop
12 - 14 July 2010 - University of Oxford, UK
19th International Symposium on Mathematical Theory of Networks and Systems
5 - 9 July 2010 - Eotvos Lorand University, Budapest, Hungary
Statistical modelling and inference for networks (Statworks)
28 June - 1 July 2010 - University of Bristol, UK
Regional Meeting on Mathematics, Computation and Biology
24 June 2010 - University of West of England, UK
iGEM Jamboree 2009
31 October - 2 November 2009 - MIT, USA
Engineering Principles in Biological Systems
14 - 16 October 2009 - Wellcome Trust Conference Centre, Hinxton, UK
ECCS 09 - European Conference on Complex Systems
21 - 25 September 2009 - University of Warwick, UK
International Workshop on Complex Systems and Networks
20 - 22 July 2009 - University of Bristol, UK
NetSci 09
29 June - 3 July 2009 - Istituto Veneto Scienze Lettere ed Arti, Venice, Italy
Regional Meeting on Mathematics, Computation and Biology
2 June 2009 - University of Bristol, UK
UK-Japan Winter School - Complexity and Dynamics
8 - 11 January 2009 - University of Bath, UK
iGEM Jamboree 2008
8 - 9 November 2008 - MIT, USA
BICS Conference - Emergence in Complex Systems
9 - 11 September 2008 - University of Bath, UK
Mathematics of Networks 7th Meeting
27 June 2008 - University of Bristol, UK
Regional Meeting on Mathematics, Computation and Biology
24 June 2008 - Hewlett Packard Laboratories, UK
From Molecules to Human Societies
7 May 2008 - Imperial College London, UK
Teaching
Predictive Life Sciences Mathematics Helpdesk (Sept 2009 onwards) - Student consultant answering questions related to general statistical methods, modelling of biological systems, high performance computer simulation, general programming, plus many other areas.
iGEM Instructor (2009, 2010) - Acted as instructor for the BCCS-Bristol iGEM team helping with idea exploration, development of mathematical models, software engineering and general administrative tasks.
Synthetic Biology Fieldcourse (2010) - Developed materials and ran a short lab session for the students to learn about agent-based modelling of bacterial systems using the BSim software.
EMAT10720 Continuous Mathematics for Computer Science (2009-10) - Assisted with examples classes covering topics such as probability theory, analysis, calculus and linear algebra.
EMAT10714 Discrete Mathematics for Computer Science 1 (2009-10) - Assisted with examples classes covering topics such as number theory, set theory, relations, functions, formal reasoning and logic.
EMAT10921 Computer Programming (2009-10) - Assisted with lab sessions covering the basics of C based programming.
EMAT202921 Additional Computer Programming (2009-10) - Assisted with lab sessions covering introductions to MATLAB/Simulink and object-orientated programming with C++.
CS132 Computer Organisation and Architecture (Warwick 2003-04) - Assisted with lab sessions covering the building of electric circuits, basic micro-architectures (68000), I/O with various lab equipment (oscilloscopes) and low-level programming for memory mapped devices.
