title: Solution of the chemical master equation by radial basis functions approximation with interface tracking.
abstract: BACKGROUND
  The chemical master equation is the fundamental equation of stochastic chemical kinetics. This differential-difference equation describes temporal evolution of the probability density function for states of a chemical system. A state of the system, usually encoded as a vector, represents the number of entities or copy numbers of interacting species, which are changing according to a list of possible reactions. It is often the case, especially when the state vector is high-dimensional, that the number of possible states the system may occupy is too large to be handled computationally. One way to get around this problem is to consider only those states that are associated with probabilities that are greater than a certain threshold level.
  
  
  RESULTS
  We introduce an algorithm that significantly reduces computational resources and is especially powerful when dealing with multi-modal distributions. The algorithm is built according to two key principles. Firstly, when performing time integration, the algorithm keeps track of the subset of states with significant probabilities (essential support). Secondly, the probability distribution that solves the equation is parametrised with a small number of coefficients using collocation on Gaussian radial basis functions. The system of basis functions is chosen in such a way that the solution is approximated only on the essential support instead of the whole state space.
  
  
  CONCLUSIONS
  In order to demonstrate the effectiveness of the method, we consider four application examples: a) the self-regulating gene model, b) the 2-dimensional bistable toggle switch, c) a generalisation of the bistable switch to a 3-dimensional tristable problem, and d) a 3-dimensional cell differentiation model that, depending on parameter values, may operate in bistable or tristable modes. In all multidimensional examples the manifold containing the system states with significant probabilities undergoes drastic transformations over time. This fact makes the examples especially challenging for numerical methods.
  
  
  CONCLUSIONS
  The proposed method is a new numerical approach permitting to approximately solve a wide range of problems that have been hard to tackle until now. A full representation of multi-dimensional distributions is recovered. The method is especially attractive when dealing with models that yield solutions of a complex structure, for instance, featuring multi-stability.
authors.affiliation: University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands. i.kryven@uva.nl.
authors.forename: Ivan
authors.initials: I
authors.lastname: Kryven
authors.affiliation: Zuse Institute Berlin, Takustrasse 7, Berlin, 14195, Germany. susanna.roeblitz@zib.de.
authors.forename: Susanna
authors.initials: S
authors.lastname: Röblitz
authors.affiliation: Freie Universität Berlin, Arnimallee 6, Berlin, 14195, Germany. schuette@mi.fu-berlin.de.|Zuse Institute Berlin, Takustrasse 7, Berlin, 14195, Germany. schuette@mi.fu-berlin.de.
authors.forename: Christof
authors.initials: C
authors.lastname: Schütte
mesh_terms: D000465:Algorithms; D001669:Biochemical Phenomena; D002454:Cell Differentiation; D025461:Feedback, Physiological; D005786:Gene Expression Regulation; D007700:Kinetics; D008956:Models, Chemical; D016011:Normal Distribution; D013269:Stochastic Processes