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Browsing by Author "Schilstra, M."
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Algebraic analysis of the computation in the Belousov-Zhabotinsky reaction
Dini, P.; Nehaniv, C.L.; Egri-Nagy, A.; Schilstra, M. (Springer Nature, 2012)We analyse two very simple Petri nets inspired by the Oregonator model of the Belousov-Zhabotinsky reaction using our stochastic Petri net simulator. We then perform the Krohn-Rhodes holonomy decomposition of the automata ... -
Are the trapping dynamics in Photosystem II sensitive to QA redox potential?
Barter, L.; Schilstra, M.; Barber, J.; Durrant, J.R.; Klug, D.R. (2001)Removal of the manganese complex from photosystem II (PSII) causes a 145 meV shift in the redox potential of the plastoquinone QA [Biochim. Biophys. Acta 1229 (1995) 193; Photosynthetica 27 (1–2) (1992) 89; Biochim. Biophys. ... -
Automatic Analysis of Computation in BioChemical Reactions
Egri-Nagy, A.; Nehaniv, C.L.; Rhodes, J.L.; Schilstra, M. (2008)We propose a modeling and analysis method for biochemical reactions based on finite state automata. This is a completely different approach compared to traditional modeling of reactions by differential equations. Our method ... -
Bio-logic: gene expression and the laws of combinatorial logic
Schilstra, M.; Nehaniv, C.L. (2008)At the heart of the development of fertilized eggs into fully formed organisms and the adaptation of cells to changed conditions are genetic regulatory networks (GRNs). In higher multi-cellular organisms, signal selection ... -
BIOMICS Project : Biological and Mathematical Basis of Interaction Computing
Dini, Paolo; Nehaniv, C.L.; Egri-Nagy, Attila; Schilstra, M.; Schreckling, Daniel; Posegga, Joachim; Horvath, Gabor; Munro, Alastair J. (2012)The main idea that led us to propose this project is inspired by the observation that cell metabolic/regulatory systems are able to self-organise and/or construct order dynamically, through random interactions between their ... -
BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems
Le Novere, N.; Bornstein, B.; Broicher, A.; Courtot, M.; Donizelli, M.; Dharuri, H.; Li, L.; Sauro, H.; Schilstra, M.; Shapiro, B.E.; Snoep, J.L.; Hucka, M. (2006)BioModels Database (http://www.ebi.ac.uk/ biomodels/), part of the international initiative BioModels.net, provides access to published, peerreviewed, quantitative models of biochemical and cellular systems. Each model is ... -
CellML2SBML : conversion of CellML into SBML
Schilstra, M.; Li, L.; Matthews, J.; Finney, A.; Hucka, M.; Le Novere, N. (2006)CellML and SBML are XML-based languages for storage and exchange of molecular biological and physiological reaction models. They use very similar subsets of MathML to specify the mathematical aspects of the models. CellML2SBML ... -
Changes in the Iron Coordination Sphere of Fe(II) Lipoxygenase-1 from Soybeans upon Binding of Linoleate or Oleate
Van Der Heijdt, L.M.; Schilstra, M.; Feiters, M.C.; Navaratnam, S.; Nolting, H-F.; Hermes, C.; Veldink, G.A.; Vliegenthart, J.F.G. (1995)Fe K-edge X-ray absorption spectra of the non-heme iron constituent of lipoxygenase-1 from soybeans were obtained. The spectrum of 2.5 mM Fe(II) lipoxygenase, mixed with 1.2 M linoleate in the absence of O2, was compared ... -
Circular Dichroism and Its Application to the Study of Biomolecules
Martin, S.R.; Schilstra, M. (2008) -
Copper(I) and copper(II) compounds of 1,7-bis(2-benzimidazolyl)-2,6-dithiaheptane (BBDHp). X-ray structure of linearly coordinated copper(I) in the cation [CuI(BBDHp)]+
Schilstra, M.; Birker, P.J.M.W.L.; Verschoor, G.C.; Reedijk, J. (1982) -
Design of spatially extended neural networks for specific applications
Adams, Roderick; te Boekhorst, Rene; Rust, A.G.; Kaye, Paul H.; Schilstra, M. (Institute of Electrical and Electronics Engineers (IEEE), 2004)The processes and mechanisms of biological neural development provide many powerful insights for the creation of artificial neural systems. Biological neural systems are, in general, much more effective in carrying out ... -
The Dioxygenation Rate in Lipoxygenase Catalysis Is Determined by the Amount of Iron( HI) Lipoxygenase in Solution
Schilstra, M.; Veldink, G.A.; Vliegenthart, J.F.G. (1994) -
Do Motifs Reflect Evolved Function? – No Convergent Evolution of Genetic Regulatory Network Subgraph Topologies
Knabe, J.; Nehaniv, C.L.; Schilstra, M. (2008-10)Methods that analyse the topological structure of networks have recently become quite popular. Whether motifs (subgraph patterns that occur more often than in randomized networks) have specific functions as elementary ... -
Does CamKII decode ca2+ oscillations?
Pinto, T.M.; Schilstra, M.; Steuber, Volker (2012)Oral presentation at CNS 2012 -
Dynamic instability of microtubules: Monte Carlo simulation and application to different types of microtubule lattice
Martin, S.R.; Schilstra, M.; Bayley, P.M. (1993)Dynamic instability is the term used to describe the transition of an individual microtubule, apparently at random, between extended periods of slow growth and brief periods of rapid shortening. The typical sawtooth growth ... -
Dynamic properties of microtubules at steady state of polymerisation
Martin, S.R.; Schilstra, M.; Bayley, P.M. (1987)Microtubules of tubulin dimer, polymerised in vitro to steady-state are shown to incorporate tubulin rapidly and extensively. The method involves adding [3H]-GTP to microtubules at steady state, and analysing for ... -
Effect of lipid hydroperoxide on lipoxygenase kinetics
Schilstra, M.; Veldink, G.A.; Verhagen, J.; Vliegenthart, J.F.G. (1992)In order to investigate the activation of lipoxygenase and to clarify the role of the oxygenation product hydroperoxide in this process, the effect of 13-hydroperoxylinoleic acid (P, 0-35 pM) on linoleic acid (S, 1-80 pM) ... -
Effect of Nonionic Detergents on Lipoxygenase Catalysis
Schilstra, M.; Veldink, G.A.; Vliegenthart, J.F.G. (1994)In many studies on lipoxygenase catalysis, nonionic detergents are used to obtain an optically transparent solution of the fatty acid substrate. In order to resolve some controversies that exist with regard to the ... -
The effect of podophyllotoxin on microtubule dynamics
Schilstra, M.; Martin, S.R.; Bayley, P.M. (1989)We have investigated the effects of podophyllotoxin on the dynamic properties of microtubules assembled from pure tubulin dimer. Excess podophyllotoxin causes the complete disassembly of microtubules, through formation of ... -
The effect of solution composition on microtubule dynamic instability
Schilstra, M.; Bayley, P.M.; Martin, S.R. (1991)The exchange of tubulin dimer into steady-state microtubules was studied over a range of solution conditions, in order to assess the effects of various common buffer components on the dynamic instability of microtubules. ...