Matthew Lakin

Matthew Lakin

University of New Mexico
Department of Computer Science
Mail stop: MSC01 1130
1 University of New Mexico
Albuquerque, NM 87131-0001

Email: <firstinitial><lastname> AT cs.unm.edu
Curriculum Vitae
Google Scholar page


Research

I am a postdoctoral scholar in the Molecular Computing Group in the Department of Computer Science at the University of New Mexico, working with Darko Stefanovic on the NSF-funded project "Computing with Biomolecules: From Network Motifs to Complex and Adaptive Systems". I am interested in the design, construction and verification of biomolecular computing devices, and in their practical application to biomedical problems such as pathogen detection and autonomous theranostics. I am also interested in the semantics and implementation of declarative programming languages.

I am partly funded by a postdoctoral fellowship from the New Mexico Cancer Nanoscience and Microsystems Training Center. I will be working with David Peabody, Steven Graves and Darko Stefanovic on applications of biomolecular logic to cancer therapy.

From 2009 to 2011 I was a postdoctoral researcher in the Computational Science group at Microsoft Research Cambridge. I worked with Andrew Phillips on programming languages and tools for biological modelling and synthetic biology such as DNA Strand Displacement (Visual DSD), the Stochastic Pi Machine (SPiM) and Genetic Engineering of Cells (GEC).

I have BA, MA and PhD degrees from the University of Cambridge. I am a member of Queens' College and I held a Munro studentship at Queens' for the 2007-2008 academic year.

I did my PhD in the Programming, Logic and Semantics Group at the University of Cambridge Computer Laboratory from 2005 to 2010. My supervisor was Andrew Pitts and I worked on the Computational Applications of Nominal Sets project. My PhD examiners were Alan Mycroft and Paul Blain Levy. My PhD dissertation is available here.

During my PhD I was lucky enough to visit Christian Urban and the Nominal Methods Group at TU München and Dan Friedman and Will Byrd at Indiana University.


Publications

Biochemical Computation

C. W. Brown III, M. R. Lakin, D. Stefanovic and S. W. Graves, Catalytic molecular logic devices by DNAzyme displacement. ChemBioChem, in press, 2014. (This paper was selected to appear on the journal cover.)
[abstract] [bib] [doi]

M. R. Lakin and D. Stefanovic, Pattern formation by spatially organized approximate majority reactions. In UCNC 2014, Lecture Notes in Computer Science, 2014. To appear.
[abstract] [bib] [pdf] [doi]

M. R. Lakin, A. Phillips and D. Stefanovic, Modular verification of DNA strand displacement networks via serializability analysis. In D. Soloveichik and B. Yurke (eds.): Proceedings of the 19th International Conference on DNA Computing and Molecular Programming, Lecture Notes in Computer Science, volume 8141, pages 133-146, Springer-Verlag, 2013. (This paper was selected as a "conference highlight".)
[abstract] [bib] [pdf] [appendices] [DOI: 10.1007/978-3-319-01928-4_10]

P. Banda, C. Teuscher and M. R. Lakin, Online learning in a chemical perceptron. Artificial Life, volume 19, number 2, pages 195-219, 2013.
[abstract] [bib] [DOI: 10.1162/ARTL_a_00105]

M. R. Lakin, A. Minnich, T. Lane and D. Stefanovic, Towards a biomolecular learning machine. In J. Durand-Lose and N. Jonoska (eds.): UCNC 2012, Lecture Notes in Computer Science, volume 7445, pages 152-163, Springer-Verlag, 2012.
[abstract] [bib] [DOI: 10.1007/978-3-642-32894-7_15]

M. R. Lakin, D. Parker, L. Cardelli, M. Kwiatkowska and A. Phillips. Design and analysis of DNA strand displacement devices using probabilistic model checking. Journal of the Royal Society Interface, volume 9, number 72, pages 1470-1485, 2012.
[abstract] [bib] [DOI: 10.1098/rsif.2011.0800]

M. R. Lakin, L. Paulevé and A. Phillips. Stochastic simulation of multiple process calculi for biology. Theoretical Computer Science, volume 431, pages 181-206, 2012.
[abstract] [bib] [DOI: 10.1016/j.tcs.2011.12.057]

M. R. Lakin, S. Youssef, L. Cardelli and A. Phillips. Abstractions for DNA circuit design. Journal of the Royal Society Interface, volume 9, number 68, pages 470-486, 2012.
[abstract] [bib] [DOI: 10.1098/rsif.2011.0343]

M. R. Lakin, S. Youssef, F. Polo, S. Emmott and A. Phillips. Visual DSD: a design and analysis tool for DNA strand displacement systems. Bioinformatics, volume 27, issue 22, pages 3211-3213, 2011.
[abstract] [bib] [DOI: 10.1093/bioinformatics/btr543]

M. R. Lakin and A. Phillips. Modelling, simulating and verifying Turing-powerful strand displacement systems. In L. Cardelli and W. Shih (eds.): Proceedings of the 17th International Conference on DNA Computing and Molecular Programming, Lecture Notes in Computer Science, volume 6937, pages 130-144. Springer-Verlag, 2011.
[abstract] [bib] [DOI: 10.1007/978-3-642-23638-9_12] [supplementary files]

A. Phillips, M. R. Lakin and L. Paulevé, Stochastic simulation of process calculi for biology. In G. Ciobanu and M. Koutny (eds.): Membrane Computing and Biologically Inspired Process Calculi 2010, Electronic Proceedings in Theoretical Computer Science, volume 40, pages 1-5. 2010.
[abstract] [bib] [DOI: 10.4204/EPTCS.40.1]

L. Paulevé, S. Youssef, M. R. Lakin and A. Phillips. A generic abstract machine for stochastic process calculi. In CMSB 2010: Proceedings of the 8th International Conference on Computational Methods in Systems Biology, Trento, Italy, pages 43-54. ACM, 2010.
[abstract] [bib] [DOI: 10.1145/1839764.1839771]

Programming Languages

M. R. Lakin and A. Phillips, Compiling DNA strand displacement reactions using a functional programming language. In M. Flatt and H.-F. Guo (eds.), Proceedings of Practical Aspects of Declarative Languages 2014, Lecture Notes in Computer Science, volume 8324, pages 81-86, Springer International Publishing Switzerland, 2014.
[abstract] [bib] [pdf]

M. R. Lakin and A. M. Pitts, Contextual equivalence for inductive definitions with binders in higher-order typed functional programming. Journal of Functional Programming, volume 23, number 6, pages 658-700, 2013.
[abstract] [bib] [pdf] [DOI: 10.1017/S0956796813000245]

M. R. Lakin and A. M. Pitts, Encoding abstract syntax without fresh names. Journal of Automated Reasoning, volume 49, number 2, pages 115-140, 2012.
[abstract] [bib] [DOI: 10.1007/s10817-011-9220-7]

M. R. Lakin. Constraint solving in non-permutative nominal abstract syntax. Logical Methods in Computer Science, volume 7 (3:06), pages 1-31, 2011.
[abstract] [bib] [online]

M. R. Lakin. An executable meta-language for inductive definitions with binders. PhD thesis, University of Cambridge, 2010.
[abstract] [bib] [pdf]

M. R. Lakin and A. M. Pitts. Resolving inductive definitions with binders in higher-order typed functional programming. In Programming Languages and Systems: Proceedings of the 18th European Symposium on Programming (ESOP 2009), York, UK, Lecture Notes in Computer Science, volume 5502, pages 47-61. Springer-Verlag, 2009.
[abstract] [bib] [pdf © 2009 Springer-Verlag] [DOI: 10.1007/978-3-642-00590-9_4]

M. R. Lakin and A. M. Pitts. A metalanguage for structural operational semantics. In M. T. Morazán (ed.), Trends in Functional Programming Volume 8. Intellect, 2008.
[abstract] [bib] [pdf © 2008 Intellect]

Dynamical Systems

A. Goudarzi, M. R. Lakin and D. Stefanovic, Reservoir computing approach to robust computation using unreliable nanoscale networks. In UCNC 2014, Lecture Notes in Computer Science, 2014. To appear.
[abstract] [bib] [PDF] [DOI]

A. Goudarzi, M. R. Lakin and D. Stefanovic, DNA reservoir computing: a novel molecular computing approach. In D. Soloveichik and B. Yurke (eds.): Proceedings of the 19th International Conference on DNA Computing and Molecular Programming, Lecture Notes in Computer Science, volume 8141, pages 76-89, Springer-Verlag, 2013.
[abstract] [bib] [pdf] [appendices] [DOI: 10.1007/978-3-319-01928-4_6]


Software


Teaching

I have previously supervised the following courses for Queens', New Hall and various other colleges in the University of Cambridge:

I use the following convention for naming tripos questions: year of examination followed by CST paper number (in roman numerals) followed by question number.


Tue Nov 19 11:08:14 MST 2013