Matthew Douglas Johnston June 12, 2016 Assistant Professor matthew.johnston@sjsu.edu Department of Mathematics johnstonmd.wordpress.com San José State University Office: DH 215 One Washington Square Phone: (408) 924-1387 San José, CA 95192 Fax: (408) 924-5080 Employment San José State University Assistant Professor San José, CA 2015 present Madison, WI Van Vleck Visiting Assistant Professor 2012 2015 Sessional Instructor 2012 Education Ph.D. Mathematics (Advisor: David Siegel) 2006 2011 Guelph, ON M.Sc. Mathematics (Advisor: Monica Cojocaru) 2005 2006 Guelph, ON B.A.H. Mathematics 2001 2005 Awards, Grants & Honors RSCA Program Grant (applied).................................. 2016 Woodward Grant (applied, pending)................................ 2015 AMS-Simons Travel Grant.................................. 2013 2015 NSERC Postgraduate Scholarship (PGS D)........................ 2006 2010 President s Graduate Scholarship............................. 2006 2010 Ontario Graduate Scholarship (OGS) (declined)......................... 2006 Mathematics Graduate Scholarship................................ 2006 NSERC Undergraduate Student Research Award........................ 2005 Wally Fraser Mathematics Scholarship.............................. 2004 Publications 13. Matthew D. Johnston, A linear programming approach to dynamical equivalence, linear conjugacy, and the Deficiency One Theorem. accepted in J. Math. Chem., 2016.
12. Matthew D. Johnston, Casian Pantea, and Pete Donnell, A computational approach to persistence, permanence, and endotacticity of biochemical reaction networks. J. Math. Biol., 72(1), 467-498, 2016. 11. Matthew D. Johnston, A computational approach to steady state correspondence of regular and generalized mass action systems, Bull. Math. Biol., 77(6), 1065 1100, 2015. 10. David F. Anderson, Germán Enciso, and Matthew D. Johnston, Stochastic analysis of chemical reaction networks with absolute concentration robustness, J. R. Soc. Interface, 11(93), 20130943, 2014. 9. Matthew D. Johnston, Translated chemical reaction networks, Bull. Math. Biol., 76(5), 1081 1116, 2014. 8. Matthew D. Johnston, David Siegel, and Gábor Szederkényi, Computing weakly reversible linearly conjugate chemical reaction networks with minimal deficiency, Math. Biosci., 241(1), 88 98, 2013. 7. Matthew D. Johnston, David Siegel, and Gábor Szederkényi, Dynamical equivalence and linear conjugacy of chemical reaction networks: new results and methods, MATCH Commun. Math. Comput. Chem., 68(2), 443, 2012. 6. Matthew D. Johnston, David Siegel, and Gábor Szederkényi, A linear programming approach to weak reversibility and linear conjugacy of chemical reaction networks, J. Math. Chem., 50(1), 274 288, 2012. 5. Matthew D. Johnston and David Siegel, Weak dynamical non-emptiability and persistence of chemical kinetics systems, SIAM J. Appl. Math., 71(4), 1263 1279, 2011. 4. Matthew D. Johnston and David Siegel, Linear conjugacy of chemical reaction networks, J. Math. Chem., 49(7), 1263 1282, 2011. 3. David Siegel and Matthew D. Johnston, A stratum approach to global stability of complex balanced systems, Dyn. Syst., 26(2), 125 146, 2011. 2. Matthew D. Johnston and Monica-Gabriela Cojocaru, Equilibria and periodic solutions of projected dynamical systems on sets with corners, Aust. J. Math. Anal. Appl., 5(2), 4 12, 2008. 1. Monica-Gabriela Cojocaru, Chris T. Bauch, and Matthew D. Johnston, Dynamics of vaccination strategies via projected dynamical systems, Bull. Math. Biol., 69(5), 1453 1476, 2007. Theses 2. Matthew D. Johnston, Topics in chemical reaction network theory, Ph.D. thesis, University of Waterloo, 2011. 1. Matthew D. Johnston, Case studies of existence of periodic solutions for projected dynamical systems on euclidean spaces, Master s Thesis,, 2006.
Teaching Experience Course Instructor MATH 133A: Ordinary Differential Equations San José State University Instructor Spring 2016 MATH 123: Differential Equations and Linear Algebra San José State University Instructor Spring 2016 MATH 133A: Ordinary Differential Equations San José State University Instructor (4.1/5 course evaluation) Fall 2015 MATH 32: Calculus III San José State University Instructor (4.1/5 course evaluation) Fall 2015 MATH 415: Applied Dynamical Systems... Instructor (4.56/5 course evaluation) Fall 2014 MATH 521: Analysis I Instructor (4.56/5 course evaluation) Spring 2014 MATH 319: Techniques in Ordinary Differential... Instructor (4.37/5 course evaluation) Fall 2013 MATH 320: Linear Algebra and Differential... Instructor (4.41/5 course evaluation) Spring 2013 MATH 415: Applied Dynamical Systems... Instructor (3.73/5 course evaluation) Fall 2012 MATH 116: Calculus 1 for Engineers Instructor (86% course evaluation) Spring 2012 SYDE 112: Fundamental Engineering Math 2 Instructor (95% course evaluation) Spring 2012 MATH 118: Calculus 2 for Engineers Instructor (92% course evaluation) Winter 2009 Teaching Assistant AMATH 453: Partial Differential Equations 2 Teaching Assistant Fall 2011 AMATH 331: Applied Real Analysis Teaching Assistant Fall 2011 MATH 117: Calculus I for Engineering Teaching Assistant Fall 2011 AMATH 250: Introduction to Differential Equations Teaching Assistant Winter 2011 MATH 228: Differential Equations for Physics and Chemistry Teaching Assistant Fall 2010 MATH 127: Calculus 1 for the Sciences Teaching Assistant Fall 2010 MATH 212: Advanced Calculus 2 for Engineers Teaching Assistant Fall 2009
MATH 137: Calculus 1 for Honours Mathematics Teaching Assistant Fall 2009 MATH 117: Calculus 1 for Engineers Teaching Assistant Fall 2008 MATH 211: Advanced Calculus 1 for Engineers Teaching Assistant Fall 2007 MATH 127: Calculus 1 for the Sciences Teaching Assistant Fall 2006 MATH 1210: Calculus II Teaching Assistant Winter 2006 MATH 2150: Applied Matrix Algebra Teaching Assistant Fall 2005 MATH 1080: Elements of Calculus I Teaching Assistant Fall 2005 Additional Teaching Qualifications and Training Teaching and Learning Symposium Wisconsin Institutes for Discovery Participant May 2015 Teaching and Learning Symposium Wisconsin Institutes for Discovery Participant May 2014 Madison Math Circle Presenter February 2014 Teaching and Learning Symposium Wisconsin Institutes for Discovery Participant May 2013 Certificate in University Teaching Teaching Certificate 2009 2011 Presentations 28. Network Approaches to the Dynamics of Biochemical Reaction Systems. AMS Spring Western Sectional Meeting University of Utah, Salt Lake City, UT (April 2016). 27. Applications of Generalized Networks to Biochemical Reaction Systems. Dynamics in Networks with Special Properties Workshop MBI, Columbus, OH (January 2016). 26. Applications of Generalized Reaction Network Theory to Biochemical Reaction Modeling. SJSU Math/Stat Research Seminar SJSU, San José, CA (November 2015). 25. Extinction and Persistence in Discrete Chemical Reaction Networks. SCU Colloquium Series SCU, Santa Clara, CA (October 2015). 24. Extinction and Persistence in Discrete Chemical Reaction Networks. AMS Central Sectional Meeting Loyola University, Chicago, Il (October 2015).
23. Extinction and Persistence in Discrete Chemical Reaction Networks. SJSU Math/Stats Colloquium SJSU, San José, CA (September 2015). 22. Exploiting Network Structure in Biochemical Reaction Models. IMACS International Conference University of Georgia, Athens, GA (April 2015). 21. Correspondence of Regular and Generalized Mass Action Systems. Joint Mathematics Meetings Henry B. Gonzalez Convention Center, San Antonio, TX (January 2015). 20. Correspondence of Regular and Generalized Mass Action Systems. SIAM Conference on the Life Sciences Sheraton Charlotte, Charlotte, NC (August 2014). 19. Stochastic Modelling of CRNs. Combinatorial and algebraic approaches to chemical reaction networks University of Portsmouth, Portsmouth, UK (June 2014). 18. Correspondence of Regular and Generalized Mass Action Systems. WVU Colloquium West Virginia University, Morgantown, WV (February 2014). 17. Translated Chemical Reaction Networks. SIAM Conference on Applied Algebraic Geometry Colorado State University, Fort Collins, CO (August 2013). 16. Stochastic Chemical Reaction Networks. Applied Mathematics Graduate Student Seminar Series, Madison, WI (October 2012). 15. Determining Weakly Reversible Linearly Conjugate Chemical Reaction Networks with Minimal Deficiency. SIAM Conference on the Life Sciences Westin Hotel, San Diego, CA (August 2012). 14. Determining Weakly Reversible Linearly Conjugate Chemical Reaction Networks with Minimal Deficiency. The 8th International Conference on Differential Equations and Dynamical Systems, (August 2012). 13. Determining Weakly Reversible Linearly Conjugate Chemical Reaction Networks with Minimal Deficiency. Algebraic Methods in Systems and Evolutionary Biology Mathematical Biosciences Institute, Columbus, OH (May 2012). (Poster) 12. Determining Weakly Reversible Linearly Conjugate Chemical Reaction Networks with Minimal Deficiency. Chemical Biophysics Symposium University of Toronto, Toronto, ON (April 2012). (Poster) 11. Linear Conjugacy of Chemical Reaction Networks. Departmental Seminar Series University of Guelph, Guelph, ON (November 2011). 10. Linear Conjugacy of Chemical Reaction Networks. Applied Mathematics Graduate Student Seminar Series, (October 2011). 9. Linear Conjugacy of Chemical Reaction Networks. SIAM Conference on Applied Algebraic Geometry Raleigh, NC (October 2011). 8. A Computational Approach to Linear Conjugacy of Chemical Reaction Networks. Applied Mathematics, Modeling and Computational Science Conference (July 2011). 7. Linear Conjugacy of Chemical Reaction Networks. SIAM Conference on Applications of Dynamical Systems Snowbird, UT (May 2011). (Poster) 6. Linear Conjugacy of Chemical Reaction Networks. Graduate Student Research Conference, (April 2011).
5. Linear Conjugacy of Chemical Reaction Networks. New Developments in Dynamical Systems Arising from the Biosciences Workshop Mathematical Biosciences Institute, Columbus, ON (March 2011). (Poster) 4. Stochastic Chemical Reaction Networks. Applied Mathematics Graduate Student Seminar Series, (2010). 3. Stability of Chemical Reaction Networks. 2nd Annual Pure and Applied Mathematics Graduate Student Conference McMaster University, Hamilton, ON (October 2008). 2. Behaviour of Chemical Reaction Networks. Applied Mathematics Graduate Student Seminar Series, (2008). 1. Applications of Projected Dynamical Systems to Vaccination Strategies. Department Seminar Series, Guelph, ON (2005). Participation in Workshops and Conferences AMS Spring Western Sectional Meeting Salt Lake City, UT University of Utah April 9 10, 2016 Workshop on the Global Attractor Conjecture San José, CA San José State University March 11 13, 2016 Dynamics in Networks with Special Properties Workshop Columbus, OH Mathematical Biosciences Institute January 24 29, 2016 Mathematics of Reaction Networks Workshop Madison, WI UW-Madison October 5 7, 2015 AMS Central Sectional Meeting Chicago, IL Loyola University October 3 4, 2015 AIM SQuaRE: Ideals in Algebraic Systems Biology San José, CA American Institute of Mathematics September 14 18, 2015 The 2015 AMMCS-CAIMS Congress Laurier University June 8 12, 2015 IMACS International Conference Athens, GA University of Georgia April 1 4, 2015 Joint Mathematics Meetings San Antonio, TX Henry B. Gonzalez Convention Center January 10 13, 2015 SIAM Conference on the Life Sciences Charlotte, NC Sheraton Charlotte August 4 7, 2014 Combinatorial and algebraic approaches to chemical... Portsmouth, UK University of Portsmouth June 23 25, 2014 SIAM Conference on Applied Algebraic Geometry Fort Collins, CO Colorado State University August 1 4, 2013 36th Conference on Stochastic Processes and Their... Boulder, CO University of Colorado, Boulder July 29 August 2, 2013 2013 Mixed Integer Programming Workshop Madison, WI Wisconsin Institutes for Discovery July 22 25, 2013
Mathematical problems arising from biochemical reaction... Palo Alto, CA American Institute of Mathematics March 25 29, 2013 SIAM Conference on the Life Sciences San Diego, CA Westin San Diego August 7 10, 2012 8th International Conference on Differential Equations and... August 1 4, 2012 Algebraic Methods in Systems and Evolutionary Biology Columbus, OH Mathematical Biosciences Institute May 7 11, 2012 Chemical Biophysics Symposium Toronto, ON University of Toronto April 13 15, 2012 SIAM Conference on Applied Algebraic Geometry Raleigh, NC NCSU October 6 9, 2011 Applied Mathematics, Modeling and Computational... Laurier University July 25 29, 2011 SIAM Conference on Applications of Dynamical Systems Snowbird, UT Snowbird Ski and Summer Resort May 22 26, 2011 Graduate Student Research Conference April 25 28, 2011 CTW: New Developments in Dynamical Systems Arising... Columbus, OH Mathematical Biosciences Institute March 22 26, 2011 AMS Spring Southeastern Section Meeting Raleigh, NC North Carolina State University April 5 6, 2009 Pure and Applied Mathematics Graduate Student Conference Hamilton, ON McMaster University October 24 26, 2008 CMS/CSHPM Summer 2005 Meeting June 4 6, 2005 Southern Ontario Dynamics Day Oshawa, ON University of Ontario Institute of Technology April 2005 Other Professional Experience Organizer for: Session on Mathematical Analysis of Biological Interaction Networks workshop, Banff International Research Station, Banff, AB, June 4-9, 2017 (w/ David F. Anderson, Anne Shiu, Casian Pantea, and Lea Popovic) Session on Dynamics of Biochemical Reaction Networks, SIAM Conference on the Life Sciences, Boston, MA, July 11-14, 2016 (w/ Nicolette Meshkat) Workshop on the Global Attractor Conjecture, San José State University, March 11-13, 2016 (w/ Elizabeth Gross, Nicolette Meshkat, and Bernd Sturmfels) Networks Seminar Series,, September 2014 April 2015 Graduate Student Seminar Series,, 2008 2010
Reviewed papers for: Applied Mathematics and Computation The American Mathematical Monthly Chemical Engineering Journal Journal of Mathematical Biology (3 papers) MATCH: Communications in Mathematics and in Computer Chemistry Mathematical Biosciences Mathematics and Computers in Simulation Symmetry, Integrability and Geometry: Methods and Applications Systems and Control Letters Qualifying exam committee for: Jennifer Beckingham (Fall 2015) Geoff Zoehfeld (Fall 2015) SJSU Department committees: Ad-hoc Applied Mathematics Masters Committee (Fall 2015-) Mathematics Research Committee (Fall 2015-) Computational Skills Markup Languages (X)HTML, L A TEX, MathML Specialized Software and Interfaces Maple, MATLAB, GLPK, SCIP, Python, C++, Desire2Learn, Canvas, WebAssign, Piazza References David F. Anderson, Associate Professor, Department of Mathematics, University of Wisconsin-Madison anderson@math.wisc.edu Gheorghe Craciun, Professor, Department of Mathematics, craciun@math.wisc.edu David Siegel, Professor, Department of Applied Mathematics, dsiegel@uwaterloo.ca Gábor Szederkényi, Senior Researcher, Computer and Automation Research Institute, Hungarian Academy of Sciences szeder@sztaki.hu Betsy Stovall, Assistant Professor, Department of Mathematics, stovall@math.wisc.edu